The American museum of natural history. American Museum of Natural History – 79th @ Central Park West
This is one of my favorite places in New York, part of the reason is the little gasps from kids walking in (I feel the same way). This museum is gigantic, you can see a diorama of a blue whale, cower under dinosaur skeletons, observe butterflies in the conservatory and then sit back and listen to Whoopi Goldberg tell you about the birth of stars. They have a lot of kid specific activities too. It can be a lot to take in if you try to see everything in one visit. My suggestion is to skip out on all the various human diorama exhibits.
