Just an FYI - staying in Jersey City at the Hyatt, you'd be paying for parking (they have valet parking - frankly, I always find street parking in JC on the weekends, but it's hit or miss), but there are other great hotels in Jersey City where I think parking would be free (like the Doubletree), and taking a bus or PATH train or ferry into the city is REALLY easy. Staying in Weehawken would be even easier - you're right on the Hudson, parking is free (double check, but the last time we stayed there, it was), and the bus to NYC is literally at your doorstep and gets you into the city in minutes. The ferry is also literally right next to the hotel.
The PATH train runs between Jersey City (and Hoboken) and NYC. There are two destinations - one takes you downtown to the WTC site, and one takes you to 33rd Street with stops in Greenwich Village and Chelsea.
Think easy - if you are driving, and plan on staying in the city, you'll have to drive into Manhattan, and pay a LOT for parking at your hotel. Some folks have suggested parking in a lot away from the hotel, but that's a complication, especially if you've never been in the city before. Also, hotel rooms in NYC tend to be much smaller than hotels outside of the city. On Priceline, they make a point to tell you that you should only plan on two people per room, and that's the truth. So if you are traveling with more than a couple, you'll want to make sure you check with the hotel if you stay in NYC, as you might get stuck.
KC