Sony Wonder Lab-- one of the best trips I've taken students on was to this interactive museum. Very hands-on, fun and informative! Plus there's a free Sony arcade in the adjacent building.
Transit Museum-- located in downtown Brooklyn, very interactive. Great for younger kids and middle schoolers.
Musuem of Moving Image-- located in Astoria Queens, this is a must as most students don't get to go here. This museum is also very interactive and informative. The kids get to do voiceovers, sound mixing, create short animations and learn about the history of TV and film.
Museum of Natural History-- one of my favorite museums in the city, though many students tire of it by the time they reach middle school. Plenty to see that aligns to science and history curricula.
Hall of Science-- located in Queens, this is a hands on science museum with an interactive, science-orientated playground. The kids love it here, and so do their teachers!
Apple Store-- one of the best trips I've taken students on was to the Apple Store on 14th street for an iMovie workshop. We learned how to create movies using photos taken with Photobooth. Our instructor was very personable and great with my special education group. We left the store with bright yellow t-shirts, and CDs containing our movies. Very cool trip with a long waiting list.
Prospect Park Zoo-- most schools trek to the Bronx Zoo, which is the largest zoo in the city, but Prospect Zoo is small enough to enjoy in one trip and still has a variety of animals. Plus, this zoo is adjacent to the beautiful Prospect Park in Brooklyn.