Without a doubt it is the "amusement park ride with underwater-controlled boats." Randy said it well. Here's a short summary of both patents and why the second one is the winner. The patents are thankfully written in understandable language but they're quite long so hopefully this is a simpler summary.
The omnimover patent requires that each "boat" is fairly small and that they're all pretty much attached back-to-back. The whole ride would be propelled by water. The chain of boats would have to all go at a constant speed and load and unload while in motion like a regular omnimover. This design doesn't allow for any rotating, which these PotC boats will be able to do. The boats would be guided by "guide channels" along the sides without any involvement from the floor, but we can clearly see that the boats are guided by the floor in this PotC ride. One big advantage of this omnimover system is that it has a high capacity. Another big advantage is that the turns are all that need to be guided by "guide channels" because every boat is connected. So the straight parts of the ride could go through open bodies of water (possibly with waves) or slide or roll up onto land. I call that... an Amphibnimover. I know, cute name, right? But seriously, there are tons of possibilities.
On the other hand, the underwater-controlled boats patent requires an underwater track that guides the boats. The front and back of each boat are both connected into the track. At certain parts, the track can split into two, with one track guiding the front of the boat and one guiding the back. If that doesn't make sense, basically, this allows the boat to rotate and move sideways or even backwards. The boats can go at their own speeds, and they can stop to load and unload (which allows for bigger vehicles). The water doesn't propel the boats, instead they are controlled by the track. Another significant advantage is that becuase the track controls the boats, there theoretically should never be a collision or a backup at the end of the ride.
So it's definitely the second patent, everything matches up perfectly with what we've seen and heard so far. The omnimover one sounds cool and I hope it doesn't just sit on the shelf for too long. But for a PotC ride, I like the choice they went with.