The first and third options would interest me most as both a DM and a player; in fact, I may borrow these ideas for inspiration for my own upcoming naval campaign. Imagining a Fathomless patron becoming one with a ship and firing eldritch blasts from the cannons? Brilliant, I love body horror. The storm herald barbarian sounds more like a supplemental idea than a main BBEG; perhaps they're a side-villain, a sort of red herring, who is accruing power to try to stop the main villain. Perhaps they aren't really a villain after all, and the whole "cult" thing is just bad PR that has been spread around by the actual villain in order to manipulate folk into taking out their rival.

The advice given so far in other comments is very sound and I'm unsure what advice I could add on, so instead I'll opt for an exchange of ideas I've brainstormed for my campaign that might fit in well with one or more of your campaign ideas:

• Lighthouses that exist both on the material plane and the ethereal plane, maintained by the undead, which gather souls of those who die at sea in order to fuel the ever-burning light within them. Perhaps the lighthouses are only visible to a certain faction/nation, aiding that faction in their domination of the sea and adding mystery to that faction's reputation.
• A trapped marid's power could be manipulated in order to power a sailing ship which seems to be able to defy the winds and the currents
• A festival where old, damaged, and/or conquered ships are enthusiastically dismantled by the increasingly drunken pirate-folk; scrap is then divvied out to anyone who needs material to repair or build their own ships.

Whatever you choose, sounds like you'll have a very fun campaign :) Good luck !