I've stayed in the Coast Guard Lodge on Staten Island (as linked to above). First class room and free breakfast thrown in for about $75 per night (2011 price). It's a straight road drive from the main gate to the ferry terminal (10 mins max) car park ($10 per day) and the free ferry service is frequent. Approx 1 hr from room to the centre of Manhatten. They should take you with mil ID and a NATO travel order.