Redditor Lavonicus spent three weekends exploring the lakes and sea in Fallout 4 mapping out where there are oddities and loot. While there are no hidden vaults or dungeons underwater there are some neat loot to be had for those who dare step into the murky radioactive waters of Boston and vicinity.
You can check out his 113 strong picture gallery on Imgur or if you want a quick guide to the loot of the sea head over to his YouTube channel for help to locate the junk/treasures.
There has been speculation that there would be some kind of underwater DLC in the future, particularly as modders found evidence of a harpoon gun, Lavonicus also suggests that a mysterious sphere could be related to this. It's of course pure speculation, but it would make sense given the amount of water in Fallout 4 that something would be hidden underneath... We'll have to wait and see what DLC plans Bethesda have.