You can also go to the South Street Seaport and purchase boat tickets to see the harbor or jump on the Staten Island for free with an unlimited Metrocard. Also, probably a fun museum would be the Children's Museum. Exhibits | Children's Museum of Manhattan
I'm trying to think hard because Manhattan is usually a place for adults, in my opinion. But, maybe you can cross the border into Brooklyn. Maybe Times Square to see a musical and take in the sights?
Maybe Central Park, a lot of people the scenery.... or FAO Schwartz toy store. Also, Prospect Park in Brooklyn has a zoo but its for kids, so they may enjoy it and they have a carousel nearby. Plan Your Trip
You can take the MTA Metropolitan Transit Authority. You can find directions on the trip planner online at mta.info | Home Page
and click on trip planner or use HopStop.com - Transit Directions: Subway, Train, Bus, ferry, Bike & Taxi
. Its 2.25 for one way trip. You can save money if you buy more rides in advance, like 10 rides or so.