You should try and work a trip through Grand Central into the visit. The whole building is beautiful, the ceiling art work and history are interesting, there are remarkably good food options, it's easy to get to and from, and the visit won't take very long which makes it perfect to hit on your way to/from other items on your itinerary.
Central Park is the best. Families always seem to have a blast renting bikes and riding around the loop, but just wandering around is great too. I live in the Upper West, mostly because of it's proximity to the Park.
If you're planning on going to the WTC, you can reserve tickets to the Memorial online for like $2, or get them day-of at the visitor center on Vesey St for free. The museum isn't open yet, but the memorial pools in the footprints of the twin towers, and the plaza are open and pretty moving.
http://www.911memorial.org/visitor-passes I've worked on the WTC rebuilding effort for the past 5 years, and visiting the 9/11 Memorial folks at the Preview Site (20 Vesey St) and then going into the Memorial plaza is much better than staring at the construction fence like people used to do for years. Plus, 1WTC (formerly the Freedom Tower) and 4WTC are almost fully skinned, and look fairly similar to their final forms, so you can get an idea of how things will look when they are done.
While you're downtown, walking from City Hall Park, across the Brooklyn Bridge, and checking out Bk Bridge Park/ Fulton Ferry Park and DUMBO is pretty cool. Grimaldi's, Juliana's (a relatively new place by the original owner of Grimaldi's) and Ignazio's all offer good pizza (none of them are Pepe's, but nothing is). Also, Brooklyn Ice Cream Factory is right there. If you don't want to walk, the East River Ferry goes to/from DUMBO to Pier 11 (just south of the South Street Seaport).
Bottom line, there is plenty to do, so don't confine yourself to Times Square.