One of the best "undiscovered" museums in Manhattan for children (and well, the whole family really!), is the Whitney museum, on the Upper East Side. This is a great place to introduce your children to the joys of going to a museum. It is small enough not to feel overwhelming, and has enough of a range of small changing exhibits to make it interesting, no matter how often you go. They have special classes that you can sign up for, and a wonderful audio tour- with stops just for kids. Go on a Friday night, and admission is pay what you wish!