Great ideas....

bookmarking

YOu didn't mention the Bronx Zoo which is bigger and has more exhibits than the Brooklyn Zoo, also the Bronx Botanical Garden is there as well.

The ToysRUs in Times Square has a ferris wheel IN the store and well worth the few dollars to ride.

There's also a carousel in Central Park and one in Bryant Park (42nd and 6th Ave).

Sounds like you are going to have a GREAT time while you are here.

The Brooklyn Children's Museum is about a mile away from the Botanic Gardens and is in a residential area.

There is something called the Heart of Brooklyn Connection run by a nonprofit. That includes free transportation to the Brooklyn sites on the weekends. It looks like it is only for the summer months.
http://www.heartofbrooklyn.org/connection/