Well, good news and bad news...
Good news is, sure you can do all that!
Bad news is, you'll have to program it yourself.
I don't know of anything that can import 3DS files into lwjgl, but there is an XML importer built into the API, and I posted a simple OBJ importer in another thread (can you export from 3DSMax out to OBJ? Most programs can).
As for the movement simulation, that gets pretty tricky. I would kind of hope that since it's your school project, that you've learned a bit about it in your class. Off the top of my head, I would say to simulate the boats track along the Y axis with a sine wave. You could then modulate the amplitude of the wave using standard functions. I'm not sure how realistic you're wanting it to be though.