I have to also recommend to take the subway - it's fast, cheap, and a fundamental part of NY.
Before you do so, check the subway map! Nothing is worse than getting hopelessly lost with such a short layover.
If you have around 4 hours, the ferry and FAO Schwarz should be a perfect combination:
1/2 hour to get onto the subway train itself (see below)
1/2 hour to take the train to South Ferry and wait for the boat itself
1 hour round trip on the boat
1/2 hour to take the subway uptown to
FAO Schwarz (your daughter should like it)(see below for directions)
1 hour 15 minutes in the US's oldest toy store
15 mins to take the subway back to Penn Station
works out well.
Map: contrary to what Google may have you believe, that little building that the tour bus is next to is the Bowling Green subway entrance.
Let me know if this is confusing.