Albright-Knox Art Gallery Buffalo
American Craft Museum New York City
American Museum of Natural History New York City
American Museum of the Moving Image Astoria (New York City)
Brooklyn Public Library (More than just a library)
Bruderhof Museum Rifton
The Buffalo & Erie County Historical Society Buffalo
Chapman Historical Museum Glens Falls
The Corning Museum of Glass Corning
Dahesh Museum of Art New York City
Dia Center for the Arts New York City
el Museo del barrio New York City
The Frick Collection and Frick Art Reference Library New York City (See this museum's unusual "virtual tour.")
George Eastman House -- International Museum of Photography & Film Rochester
Georgi Museum & Park Center Shushan
Hammond Museum & Japanese Stroll Garden North Salem
Harbor Defense Museum Fort Hamilton, Brooklyn
The Hispanic Society of America New York City
The Hudson River Museum Yonkers
The Isamu Noguchi Garden Museum Long Island City
The Jewish Museum New York City
Long Island Children's Museum Garden City
Lower East Side Tenement Museum New York City
The Lucy-Desi Museum Jamestown
Madame Tussaud's Wax Museum New York City
Memorial Art Gallery of the University of Rochester
The Metropolitan Museum of Art New York City
The Morgan Library New York City
The Museum for the Preservation of Illustrative Art Marlboro
The Museum of American Folk Art New York City
Museum of Jewish Heritage New York City
The Museum of Modern Art New York City
The Museum of Television and Radio New York City
The Museum of the City of New York
The National Museum of Dance Saratoga Springs
National Warplane Museum Horseheads
Neuberger Museum of Art Purchase College, Purchase
New Museum of Contemporary Art New York City (See also the Visible Knowledge Program -- a high school outreach program of the New Museum.)
The New Netherland Museum & Half Moon Visitor's Center Albany
The New York Museum of Transportation West Henrietta
New York State Museum Albany
NYU's Grey Art Gallery New York City
The Old Stone Fort Museum Schoharie
The Parrish Art Museum Southampton
Queens Museum of Art Queens (New York City)
Roberson Museum & Science Center Binghamton
Rockwell Museum Corning
Schein-Joseph International Museum of Ceramic Art Alfred (New York State College of Ceramics at Alfred University)
Schenectady Museum & Planetarium
Shaker Museum and Library Old Chatham
The Solomon R. Guggenheim Museum New York City (Site includes direct links to four additional Guggenheim museums around the planet.)
Sony Wonder Technology Lab (This is not really a museum, but looks as though it has a lot in common with a Science Museum) New York City
Southeast Museum Brewster
The Strong Museum Rochester
Whitney Museum of American Art New York City