Across

2. The lowest part of a vessel's hull, where any water in the hull collects.
Bilge

3. A person who navigates a vessel. Historically another name for Navigator, usually different from the Master or Captain.
Pilot

4. Floors on a ship. Each level is called this.
Deck

6. The middle of the ship, either lengthwise or widthwise, or both.
Amidships

8. The left side of a vessel. This side of the ship traditionally pulls to the dock.
Port

9. The top rail of the side of a boat or ship. 
Gunwale

10. The back of a vessel.
Stern

11. Toward the rear of the ship
Aft

12. The front of a vessel.
Bow

Down

1. The front part of a ship.
Fore

2. Any heavy material such as lead, concrete, or stones placed low in a vessel to increase stability.
Ballast

5. A person who pilots the ship in specific bodies of water.
Captains

7. The outer body or shell of a vessel, floating partially immersed in water and supporting the remainder of the vessel.
Hull

10. The right side of a vessel. The team is derived from "steering board" a large, paddle-shaped board used to steer ancient boats. Traditionally this board was on the right side of the ship.
Starboard

Source:  http://www.puzzlemaker.com