Well, as a passenger you could say you're riding on a bus or train, yes, just as you ride in a car. I don't think you ride on a ship, but maybe on a boat.
More often, you skip the verb and just say you are on the bus, train, or ship, since it's relatively obvious what you're doing on it. Only perhaps with a small child: Look, grandma, we're riding (on) the train! We're taking a train ride!
Similarly, of course the question is also not usually whether you're riding or driving, just whether you will take the bus, train, or ferry, or indeed, go by bus, train, or ship.