Only blocks away from the Brooklyn Cruise Terminal they built the Comfort Inn. This brand new property allows you to spend your night before the cruise only minutes away from the ship. You don't want to have to drive through the Battery Tunnel from Manhattan before you encounter TSA and security, pick up your room cards, and actually board a ship like the Queen Mary 2. The Comfort Inn unfortunately doesn't have a restaurant in a locale where you're not close to any eatery, but in New York City everybody delivers. Our dinner the night before the cruise was supplied by Mark's Pizzeria which was just around the corner and delivered with lightning speed. At least the hotel offers CP the morning of the cruise, but it's downstairs in a basement with window wells and looks institutional.
Tip: I would choose the lowest floor. It's closer to the lobby and breakfast.