He's usually in the broken bow of the ship swim out in the water roughlt where the ship is broken in half go under water and you'll see an under water door head through that and into the ship, you'll have to fight off a few mirelurks but you'll eventually find him in his lab, by the way there are a few booby traps before you get to him so watch out make sure to look around before touching anything.
Also the room you enter if you swim, is filled with gas.
So no laser fire or shishkabobbing the Mirelurks.
I went in the side door, from the dock.
Pick the lock, disarm 2 mines, 2 shotguns, and that's it.
You don't even see a Mirelurk, unless you hang around.
Right as you enter though, grab the scoped .44 and lots of ammo
in that first room.
Pinkerton is actually necessary for 2 side quests, I found him
for the Wasteland Survival Guide, and then after finishing
that proceeded to question him on The Replicated Man.
