Boutique hotels in Jefferson County

Find and book unique boutique hotels on Airbnb

Top-rated boutique hotels in Jefferson County

Guests agree: these boutique hotels are highly rated for location, cleanliness, and more.

1 of 1 pages1 / 1
Guest favorite
A spacious sleeping area is enhanced by a wooden ceiling, creating an inviting ambiance. Large glass doors open to a balcony, allowing natural light to fill the room. A bedside table holds a potted plant, and a soft area rug complements the flooring.
Hotel room in Clayton
4.94 out of 5 average rating, 115 reviews

Island Bay Waterfront Captains Suite

Our one of a kind location is nested right on the edge of the Village of historic Clayton, with our upstairs studio style suite overlooking our waterfront lawn and dock area, unique with great views and centrally located right in the heart of the 1000 islands area. New from top to bottom with all amenities and private balcony with dockage right in front available, a boaters dream! King size bedroom with Full kitchenette with all the essentials with full 2 couch living area with modern amenities!

FamilyValueDecor

Guest favorite
A spacious bedroom features a large, neutral-toned bed and matching light wood nightstands. A decorative woven wall piece is positioned above the bed, with a soft area rug delineating the space. Natural light fills the room, aided by minimal window coverings.
Hotel room in Clayton
4.86 out of 5 average rating, 21 reviews

Island Bayside "Getaway Grotto" room

Our ”Fisherman’s Grotto” unit is right on the edge of the Village of historic Clayton, our downstairs unit overlooks our waterfront lawn and dock, unique with great views and located right in the heart of the 1000 islands area. New from top to bottom with all amenities, Smart tv, WiFi, heated towel rack,deck and patio, dockage right in front available for extra charge, a boaters dream! Super comfortable King size bed with all the essentials, enjoy a hot Keurig coffee as well as microwave/fridge

LocationFamilyAccess

Guest favorite
A well-lit room features a large window with a view of greenery, complemented by a wooden ceiling. A compact kitchenette is equipped with a coffee maker and a small refrigerator. A comfortable chair is positioned near the window, and a cozy bed adds to the inviting space.
Hotel room in Clayton
4.9 out of 5 average rating, 112 reviews

Island Bay Waterfront -River View Room

Welcome to the Island Bay stays! Right on the edge of Historic Clayton NY, enjoy our super newly renovated waterfront “Aparthotel” style stay! Our elevated well insulted rooms and suite apartments have all the newest amenities to keep you connected and even better yet, disconnecting and relaxing to take in the 1000 islands by land or boat! Centrally located, less than a 10 min walk to downtown, Dockage available, with boat ramp and Clayton Marina and boat rentals right across the way!

ValueLocationAmenities

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 7

The Pine Street Inn — Cozy, Stylish, and Affordable Welcome to The Pine Street Inn, your home away from home where comfort meets convenience in a warm, affordable setting. Perfect for traveling professionals, military personnel, and long-term guests, our inn offers a cozy place to rest and recharge after a busy day.

LocationAmenities

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 1

The Pine Street Inn — Cozy, Stylish, and Affordable Welcome to The Pine Street Inn, your home away from home where comfort meets convenience in a warm, affordable setting. Perfect for traveling professionals, military personnel, and long-term guests, our inn offers a cozy place to rest and recharge after a busy day.

ValueLocationHospitality

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 2

The Pine Street Inn — Cozy, Stylish, and Affordable Welcome to The Pine Street Inn, your home away from home where comfort meets convenience in a warm, affordable setting. Perfect for traveling professionals, military personnel, and long-term guests, our inn offers a cozy place to rest and recharge after a busy day.

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 6

The Pine Street Inn — Cozy, Stylish, and Affordable Welcome to The Pine Street Inn, your home away from home where comfort meets convenience in a warm, affordable setting. Perfect for traveling professionals, military personnel, and long-term guests, our inn offers a cozy place to rest and recharge after a busy day.

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 4

The Pine Street Inn — Cozy, Stylish, and Affordable Welcome to The Pine Street Inn, your home away from home where comfort meets convenience in a warm, affordable setting. Perfect for traveling professionals, military personnel, and long-term guests, our inn offers a cozy place to rest and recharge after a busy day.

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 5

The Pine Street Inn — Cozy, Stylish, and Affordable Welcome to The Pine Street Inn, your home away from home where comfort meets convenience in a warm, affordable setting. Perfect for traveling professionals, military personnel, and long-term guests, our inn offers a cozy place to rest and recharge after a busy day.

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 3

The Pine Street Inn — Cozy, Stylish, and Affordable Welcome to The Pine Street Inn, your home away from home where comfort meets convenience in a warm, affordable setting. Perfect for traveling professionals, military personnel, and long-term guests, our inn offers a cozy place to rest and recharge after a busy day.

Guest favorite
A spacious room features a wooden ceiling and blue walls. A large wooden bed is positioned near a wall-mounted television. A small bedside table with a lamp stands next to the bed, and a decorative sign spelling 'RELAX' is visible on a dresser.
Hotel room in Clayton
4.98 out of 5 average rating, 84 reviews

Island Bay Waterfront - Relaxing Balcony room

Our newly available space include stylish comfortable amenities, sparkly clean room located right on the edge of Clayton is close to must-see destinations and located right on the water tucked in a bay right off Rt12

LocationValueAccuracy

Popular amenities for Jefferson County boutique hotels

WifiPoolFree parking on premisesAir conditioning

Family-friendly boutique hotels

Guest favorite
A spacious sleeping area is enhanced by a wooden ceiling, creating an inviting ambiance. Large glass doors open to a balcony, allowing natural light to fill the room. A bedside table holds a potted plant, and a soft area rug complements the flooring.
Hotel room in Clayton
4.94 out of 5 average rating, 115 reviews

Island Bay Waterfront Captains Suite

ValueLocationGetting around

Guest favorite
A well-lit room features a large window with a view of greenery, complemented by a wooden ceiling. A compact kitchenette is equipped with a coffee maker and a small refrigerator. A comfortable chair is positioned near the window, and a cozy bed adds to the inviting space.
Hotel room in Clayton
4.9 out of 5 average rating, 112 reviews

Island Bay Waterfront -River View Room

ValueFamilySolo travel

Guest favorite
A spacious room features a wooden ceiling and blue walls. A large wooden bed is positioned near a wall-mounted television. A small bedside table with a lamp stands next to the bed, and a decorative sign spelling 'RELAX' is visible on a dresser.
Hotel room in Clayton
4.98 out of 5 average rating, 84 reviews

Island Bay Waterfront - Relaxing Balcony room

ValueLocationView

Guest favorite
A spacious bedroom features a large, neutral-toned bed and matching light wood nightstands. A decorative woven wall piece is positioned above the bed, with a soft area rug delineating the space. Natural light fills the room, aided by minimal window coverings.
Hotel room in Clayton
4.86 out of 5 average rating, 21 reviews

Island Bayside "Getaway Grotto" room

LocationFamilyAccess

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 7

LocationAmenities

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 1

LocationValueHospitality

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 2

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 5

Other boutique hotel vacation rentals

Guest favorite
A spacious sleeping area is enhanced by a wooden ceiling, creating an inviting ambiance. Large glass doors open to a balcony, allowing natural light to fill the room. A bedside table holds a potted plant, and a soft area rug complements the flooring.
Hotel room in Clayton
4.94 out of 5 average rating, 115 reviews

Island Bay Waterfront Captains Suite

ValueLocationQuiet

Guest favorite
A well-lit room features a large window with a view of greenery, complemented by a wooden ceiling. A compact kitchenette is equipped with a coffee maker and a small refrigerator. A comfortable chair is positioned near the window, and a cozy bed adds to the inviting space.
Hotel room in Clayton
4.9 out of 5 average rating, 112 reviews

Island Bay Waterfront -River View Room

ValueFamilyAmenities

Guest favorite
A spacious room features a wooden ceiling and blue walls. A large wooden bed is positioned near a wall-mounted television. A small bedside table with a lamp stands next to the bed, and a decorative sign spelling 'RELAX' is visible on a dresser.
Hotel room in Clayton
4.98 out of 5 average rating, 84 reviews

Island Bay Waterfront - Relaxing Balcony room

LocationValueParking

Guest favorite
A spacious bedroom features a large, neutral-toned bed and matching light wood nightstands. A decorative woven wall piece is positioned above the bed, with a soft area rug delineating the space. Natural light fills the room, aided by minimal window coverings.
Hotel room in Clayton
4.86 out of 5 average rating, 21 reviews

Island Bayside "Getaway Grotto" room

LocationFamilyCleanliness

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 7

LocationAmenities

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 1

LocationValueWalkability

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 2

Superhost
Hotel room in Watertown

The Pine Street Inn - Room 6

Destinations to explore