If I had only 2 days my plan would be:
Day 1 - Intrepid then cab up to American Museum of Natural History. From there walk around through the park and maybe even a quick visit to the zoo if your doing well for time. Then through the park to the MET and/or the Guggenheim. If you're there around the evening the MET has a bar on the roof with nice views over the park and surrounds, would be worth stopping for a drink (I did!). Then I'd head to the observation deck of 30 Rockefeller Plaza, similar view to the Empire State but further up-town (and smaller queues). You could also have a walk around Times Square as it's pretty close to 30 rock.
Day 2 - Downtown, check out Wall St then down to Battery Point where the ferries to the Statue of Liberty leave from. When I was there around the same time 2 years ago the lines for the ferry tours were well over 2 hours long so I ended up just taking a round trip on the Staten Island ferry instead. The Staten Island ferry doesn't go to the statue but it sails past about 150m(?) away. It's also a good way to see alot of the lower harbour that you wouldn't normally see. Then up to little Italy for lunch. Then up to Times Square and across to 5th Ave (if you didn't do it already). After dinner finish off with a trip up the Empire State.
Obviously there are a million other things to do but I'd be happy with this for 2 days.
It's a great city to walk around in but if you're time-poor then cabs are cheap, you can go from downtown up to Times square for probably less than $10.
Have fun!
