I did a helicopter tour with Liberty in October and it was well worth the money. Had excellent views up the Hudson, over the Statue, Ellis Island and Manhatten. A good 13 minute flight in an A-Star. It is a shame about the Intrepid, wanted to see it as missed it in 2005, looks very strange as it is not there!
I can also highly recommend the subways, used them all the time as it is only $2 per ride to go where ever you want. One thing that is definetly worth it, is walking into Manhatten over the Brooklyn Bridge as you get fantatic views of the skyline. Also, if you want to do tours, the Grey Line buses (which are actually red) make good value, 48 hours pass to do all tours, uptown, downtown, Brooklyn, night loop, is about $50 and you can get on and off as much as you like.
If you like your food, I can definetly recommend a visit to Juniors on West 45th between Broadway and 8th Avenue, they make the best cheesecake I have ever tasted.