We already have The Boiling Rock but the (not as terrible as you would think but still pretty terrible) GI Joe movie gave me another idea for a sea-based prison. They lock Cobra Commander and Destro up in fancy laser-cages in the hull of an aircraft carrier at sea.
The prison ship would not be an aircraft carrier. In fact, it does not possess any alternate means of transportation (no helipad, no lifeboats, etc). In a fantasy setting, the ship might not even have doors leading inside. Supplies are dropped hours ahead in the path of the ship and are collected by guards or even the prisoners over the side of the hull without the supply ship coming within sight. The ship travels an endless circuit in the midst of the ocean, never approaching within a few hundred miles of islands or the coast. The message is plainly that if you are on this ship, heading into the water is a good way to be lost to death.
Of course, such a prison ship leaves many open questions. Are there guards on the ship? If so, do they get breaks or vacation and how are they replaced? How are new prisoners brought to the ship? What stops the prisoners from staging a riot and gaining control of the ship? Since there are no other ships within sight (to prevent prisoners from swimming over and stowing away), how would anyone respond to the prisoners taking control of the ship?
Lots of problems, many of which are easily solved in a fantasy setting. Prisoners are teleported into the sealed, magically guided ship that provides food or even a field of sustenance.