The other answers touched on this, but let me just spell it out more -- even if I'm not combusting anything, doing anything electronic, or carrying anything, there is a prohibition called Techum Shabbos -- (lit. "the domain"). I am prohibited from walking ~1 mile past the limits of the city where I was located on Friday night. If you are a good walker and/or live near the edge of your city, you could violate Techum just by walking a lot!
So a bus all over Brooklyn would remain within the city limits and thus (in and of itself) within Techum. (A Greyhound bus from St. Louis to Chicago, on the other hand, would violate Techum.) Embarking on almost any ship is bound to violate Techum, unless it is staying very, very close to the shoreline of an inhabited area the whole time (e.g. a yacht circumnavigating Manhattan).
(For this reason, if a ship was far out from land at dusk on Friday, then arrives into port on Shabbos morning, the "home city" of the passengers is now the ship, and they are prohibited from disembarking on Shabbos as that also would be a case of breaking Techum.)
There are other issues, as other answers referenced -- seasickness; the likelihood someone would need to save your life if something went wrong -- but the clear difference between bus and boat (in most cases) is Techum.