The wife and I are driving, arriving Dec 28th, heading back on the 31st. Staying at Fairfield Inn East Rutherford Meadowlands, got it direct from Marriott.com for $114 a night (refundable in case of weather travel issues), which includes 2 R/T bus tickets per day for NJ Transit stop right next to hotel, which takes us into Port Authority Bus Terminal.
We lived in DC from 2005-2009 and took a number of trips up to NYC. Definitely concur with other posters who are saving some money by staying in Secaucus/East Rutherford. Generally free parking around the hotels, and the NJ Transit buses into Port Authority are comfortable and reasonably quick. Looks like the last return trip from Manhattan for bus 163 leaves at 1:20AM each night, so that should give us plenty of time to enjoy the night sights.
This may be an obvious idea, but don't forget about the Broadway and off-Broadway musicals and plays if you're into that sort of thing. On our last trip there we stopped at the Times Square TKTS booth that sells day-of-show tickets, looked at the list of shows and somewhat randomly decided to see Rock of Ages at an off-Broadway theatre for a reasonable price, it was a good time. This time it may be tempting to see if there's anything reasonable available for Book of Mormon (the musical by the South Park guys), though that's probably still popular, especially this time of year.
We also took a tour of Ellis Island, which was really interesting. I think someone else in this thread recommended it over Statue of Liberty, and I would agree if you only have time for one of those two.
Finally, one thing not to do: "skating" on fake ice made of plastic. When we last visited a few years ago, the American Museum of Natural History had an outdoor skating rink that was a lot cheaper than the famous Rockefeller Plaza rink, so we decided to try it out. It was designed to be an eco-friendly rink that used no water and instead had a synthetic surface that was supposed to be a suitable substitute. Definitely a case of getting what you pay for, however, as it was impossible to skate on compared to real ice. I'm no Dorothy Hamill, but I can generally stay upright on ice skates. That rink was no fun and a waste of money.
Go Clones!