Do this by adding two new quest lines, the player must choose one or the other to stick with.
They are both different and have different aspects, features and rewards.
One is to do with piracy, the other is to do with the Navy.
The former; you join a pirate crew, and raise yourself in the ranks until you eventually convince the crew to mutiny and you become the Captain and then upgade your ship and crew. You then raid ships (from the East Empire Company and the likes) on the High Seas of Skyrim!
The latter; you join the Skyrim Navy (either Legion or Stormcloak depending on your ending) and join a ship, you defend the trade ships and raise yourself in the ranks eventually becoming Captain of the Ship.
It doesn't end when you become Captain, after that you can start buying other ships and crew members to populate them.
Eventually you can either have a fleet of maybe 3-5 ships that defend/attack trade ships - making money for you!
You can direct only one ship in a battle at a time though, but you can control what your other ships do from your HQ on-shore (a command post for the Navy and a secret cave for the Pirates).
I think it would be a cool DLC to add more to the Seas of Skyrim and have a Dovaahkin that rules the high Seas! Yarr!
Thanks for reading.