Even after six years of living in New York, there were still many things that we never had a chance (or made the effort) to see. At least three of those were museums, and we visited them during our visit in September.
Intrepid Sea, Air & Space Museum
This aircraft carrier turned museum is on the Hudson River, just west of Times Square. I found the walk-through submarine particularly interesting, and Edith enjoyed the "Explorium" and its interactive displays -- particularly climbing into the helicopter. Plenty of planes on the deck to look at, too.
New York Transit Museum
Located just a short walk from Paul's old office in Brooklyn, the museum is actually located underground in an old subway station. A short walk-through history ended in some rather extensive displays, including old turnstiles and probably dozens of former subway cars through the years. Buses weren't left out -- Edith could have spent all day in the driver's seat, pretending to steer.
Brooklyn Children's Museum
Edith had a blast (and I had a surprise, running into an old Bay Ridge friend there). I liked World Brooklyn the best, with toddler replicas of international stores throughout Brooklyn. We also spent quite a bit of time in the water, sand and gardening areas. It's basically a smaller COSI, but it was a pleasant excursion for a rainy day.