Seriously, how big is the boat, what kind of speed required? Possibly use an off-the-peg submersible? Batteries in boat or batteries in unit? just propulsion or steering as well? Interesting thoughts.
I recently bought some very small but amazingly powerful magnets, it crossed my mind that it would be possible to use them as a drive system by having two flat rotors, each with 3 magnets attached one inside and one outside of a waterproof casing thus doing away with a shaft and seal.