I haven't been overly impressed with the New York Children's Museum as a museum. Perhaps their programs for schools are different, but when our family has gone there on the weekends there exhibits/acitivities haven't struck me as particularly educational. More like fun play areas tied in with a book or tv show (e.g. Dr. Seuss or Dora).
That said, we don't really regret the money ($145) we payed for a family membership (which gives you unlimited use). Because if you have young kids (4 and under), CMOM is a kick ass indoor play area. Your child will easily be able to kill 2 hours there, which is quite a nice option to have on days with inclement weather.
Plus, there is Zabar's, Barnes and Noble, and the Museum of Natural History (a real museum!) within a few blocks.