We've found parking at Cape Liberty very easy. There is only one cruise ship dock. It is well marked. The drop area is well staffed and the parking is close by. If you can, find a space close to the terminal building.
There are shuttle buses to and from the lot,but if your physically up to towing them back to the car it makes it much easier to get your bags off the ship when you head home!
I've read rumors of over-spray from the Naval yard damaging cars, but have not had any problems.