If you are trying to take a photo where you can see the lights AND see the ship, Try this;
camera set on auto. on a tripod. Room lights off. Flash OFF boat lights ON. This will give afairly long exposure. Take a couple of shots to see how long it takes to take the picture.
Then whilst taking a picture (that is to say when the shutter is still open on the camera), do one of two things. After the first few seconds, either fire the flashgun; if it is a seperate one, or take a photo with another camera WITH a flash.
The long exposure time on the main camera will get the lights on the boat, the flash will do the rest and make the shutter on the camera close.
Sounds confusing, but giv it a few tries pointing the flash in different directions.
Another real good tip: OPen a Photobucket account, Its free and it works!