Some kind of solar powered boats with kite-sails could be interesting, but I doubt that would really scale to cargo transport. Although kite-sails for cargo ships do exist and apparently reduce fuel consumption by a low double digit percentage.
I also once read that submarines could have amazing fuel efficiency (similar to whales), so maybe some sort of fully automated slowly moving electric submarine could be feasible? In general the water drag grows in exponent with the speed, so slower moving cargo ships should be in theory a lot more fuel efficient and an automated submarine wouldn't have to worry about adverse weather etc.