Libertalia

From the Nahant Wharf side, the first boat has an Expert door with ammo boxes, crate, and an Advanced safe inside. Each boat has a container of some sort so make sure to check every boat you transfer to.

In the tower connected to the “restaurant” boat to the western side of the flotilla, there's an Advanced Safe and Terminal. You can use the terminal to unlock the safe beside it.

There's a cooking station by the beached boat SW of the flotilla. The boat in the middle with a wooden shack on the roof has an Expert safe inside. Weapons workbench on the way to the main base.

To reach the main base, you have to swim towards and use the ramp to climb the stairs. There's an armor workbench and checm station inside. The territory's boss, Wire is found on the topmost level.

In the upper level of the main base, there's an overlook with a table and red couch. You should find an issue of U.S. Covert Operations Manual there. In the same level, there's a room with an Advanced safe.

In the top level, you'll find the door to the Captain's Cabin. Inside, you'll find a novice terminal, the unique shotgun Le Fusil Terribles, and the mini-nuke under the shelf in the storage room. There's a ladder nearby that gives you access to the rooftop

In the rooftop level, there's a red steamer trunk, raider Power armor, Master terminal and a safe that can only be opened from the master terminal.