[quote name='lordwow']If you've never been before, you should probably check out Times Square and Rockafeller Center. Probably stuff you'll only need to see once. (The Nintendo store is a real letdown though)[/quote]
Haha, how is Times Square something you only need to see once? It's pure chaos, no doubt. But some of the best stores are there (Virgin Megastore, Toys R Us, Hard Rock, etc.) I think it's a necessary evil for even most New Yorkers.
As far as touristy things that you will only want to do once, the Statue of Liberty and Empire State Building will really suck your day away. Thanks to the terrorists, security at those places is basically airport level. They're still amazing sites to see (and things everybody probably should see), but it takes a lot more time and effort than it used to.
Chinatown is also chaos incarnate. But at least there you can get some cheap deals on really great stuff. 3 for $10 t-shirts, knockoff designer crap, and a lot of the same stuff you just saw in the SoL and ESB gift shops for about a third of the price.
If you're looking for cheap places (and why wouldn't you be? This is CAG after all), you can get into the Museum of Natural History for basically free (technically a donation...at least give them something). Central Park is also a good, cheap way to spend an afternoon...especially if you're up around the museum. John Lennon's apartment and Strawberry Fields is right by there.
Ah, I could go on and on, haha. I love New York. I'm going again in May, and hopefully will be moving there in the next year or two. Anyway, hope that gives you some ideas. You guys should have a great time.
EDIT - Oh, also, as far as getting around the City, not sure how long you're going to be there, but to keep things cheap, I always recommend using the subway. It can be intimidating for first timers, but you're from Philly, so it shouldn't bother you. You can get a one day, unlimited use Metrocard for $7.50. It works for all trains and local bus rides. You both need your own though because the card can only be swiped once every 15 minutes or something, so the "pass it back" method won't work (I learned that the hard way years ago, haha). An unlimited 7 day Metrocard is $25. For comparison, riding the train once, one way costs $2, so the unlimited cards really become a hell of a bargain very fast. You can use
www.hopstop.com to plan out which trains to catch and where. It's like Mapquest for public transportation, haha.