Stony Brook is home to the Long Island Museum of American Art, History and Carriages. Recognized as "A National Treasure in Historic Stony Brook Village", this museum contains over 40,000 items dating from the late 1700s to the present and offers afterschool services and a membership plan. The History Museum displays permanent and changing exhibitions which bring to life Long Island's history and its relation to American culture. The Art Museum features art from the museum's collection as well as traveling exhibitions, including the largest collection of works by renowned genre artist and Stony Brook resident, William Sidney Mount. The Carriage Museum features 10 galleries housing the museum's collection of over 200 horse-drawn carriages, widely recognized as the best in the United States.

At the Museum of Long Island Natural Sciences visitors can see displays of Long Island's natural history and rocks. Its mission is to promote education, research, and public service in the natural sciences. The museum features a seismometer, programs and workshops, exhibits on the geological history of Long Island, Long Island's freshwater, Long Island Sound, and geologic time. Admission is always free. They also offer themed birthday parties like a Dinosaur Party and a Native American Party.