If it was a rolling boil, it would also be possible for the water to unable to support the ship anymore and it would sink. There have been cases of gas released from the ocean floor lowering the density of the water to the point that a ship will swamp.
painandgreed beat me to it. I've seen some physics demos that show that effect- the boiling water is so much less dense than the normal water that the ship sinks rapidly due to lost bouyancy.
BTW, you get similar effects sailing/swimming across a boundary of fresh and salt water.