My thoughts on NYC:
Subway is most likely your best chance of getting anywhere around the city. The maps are not hard to read, and most subway riders are more than helpful in helping you get around.
For those suggesting the Empire State Building, be forwarned that when visiting the observatory they force you to have your picture taken and insist that you purchase it from them. I think it has something to do with a security measure, but for me, it's a real turn-off. I hope Top Of The Rock doesn't follow that suit.
And speaking of Rockefeller Center, I don't know if the skating rink will be up, but there's this neat little boutique that sells all Nintendo merchandise (games, consoles, toys, apparel, etc.). It used to be the Pokémon Center, but they redid it, and it doesn't look too bad.
But none of those midtown tourist traps can compare to my personal pick of NYC attractions: The Museum of Comic and Cartoon Art (MoCCA). Located just south of Houston St, MoCCA represents all that there is about comics and cartoons as an artform in all forms of the medium, with a heavy focus on comic art. It has gotten alot of press regarding exhibits like "Cartoons Against the Axis" (WWII propaganda cartoons as part of an actual show in the 40's to help promote the sale of war bonds) and "Will Eisner: A Retrospective", and with its appearance at this past New York Comic Con, MoCCA has grown stronger than ever. In addition to their exhibits, they have some interesting programs and lectures every Monday evening. They even have classes scheduled for this coming Spring.
I have been to this museum, I have seen all their exhibits, I've even been to their annual Art Festival last year. The Museum of Comic and Cartoon Art is one place in NYC not to be missed. If you want any more info, PM me.
Have a nice trip into NYC!