East End Seaport Museum & Marine Foundation
- Preserves the maritime heritage of the area and includes gift and blacksmith shops. Calendar of events, newsletter, children's events, and member and volunteer opportunities. Located in Greenport.
- http://www.eastendseaport.org/

Museum of Long Island Natural Sciences
- A museum dedicated to preserving and interpreting the natural heritage of Long Island.
- http://www.geosciences.stonybrook.edu/museum/

Long Island Maritime Museum
- Preserving Long Island's regional maritime heritage for educational purposes. Information on oysters, shipwrecks and great events.
- http://www.limaritime.org/

American Airpower Museum
- A museum commemorating the World War Two big iron birds, especially the Republic P-47 "Thunderbolt". Site has good info and photos of WW2 aircraft.
- http://www.americanairpowermuseum.com/

Hicksville Gregory Museum
- Housed in the historic Heitz Place Courthouse, and dedicated to providing exhibits and a range of science and craft workshops for children and adults.
- http://www.gregorymuseum.org/

The Vanderbilt Museum
- Museum and planetarium. Was the residence and museum built for William K. Vanderbilt II, great-grandson of New York's famed railroad and shipping magnate "Commodore" Cornelius Vanderbilt.
- http://www.vanderbiltmuseum.org/

Cradle of Aviation Museum at Mitchel Center
- Designed to stimulate and educate the public about Long Island's role in the history and development of aviation and space technology.
- http://cradleofaviation.org