Personally, I would vote for parking outside of NYC and taking a train or ferry in, but I'm not sure of all of the details in NJ transit parking lots. I just take the train into New Brunswick and from what I hear parking is a big pain in the ass. You can take ferries from Hoboken, Weehawken, and Jersey City, which is great fun and cheap, but parking isn't really any better in any of those places and I'd be willing to bet that the garages there are roughly the same prices as Manhattan. Staten Island might be an option, and the ferry is free - is PoSI lurking anywhere?
Alternately, you could take the Holland Tunnel in and find parking somewhere in Chinatown, which empties out at sunset, though driving on Canal Street is a bit of a nightmare.
I've taken both the Greyhound and Chinatown buses from DC and neither was all that painful - just load your Zune with a couple of episodes of the Best Show and you're set.