For the camps with enemies spawned inside the buildings:
Bomb the hell out of them...or 2h mace power swings.
Then there are those pirates on cannons that cannot persuaded to unseat themselves (since they take no damage from ranged attacks). We have to get up to them and hit them with a melee attack to unseat them. It helps to always bring a grappling hook with you as it will allow you to get to the roof tops. If you find a base with a cannon on top of a tower that has walkways on every side you will have to shimmy up, swing back, then jump to launch yourself over it. Or...you know...swing back and forth from the nearby flag then propel yourself straight at the cannon. Whichever works best for you indy.
For the ships:
It's not that they take no damage, it's more like they heal obscenely fast. (3 of us managed to get onto the schooner, break the mast to 0 and it gets repaired to full in a minute.
You can always mortar the ships if you are able to make them. If you are not, i have found that leading them to shallows with a raft works well. Build a ship cannon close by, build a door way to block shots, and continuously pepper them while they concentrate on the raft and then you.
I've never tried Harpoons...Will they work?