Ok, I found this:
I found a near sure-fire way to get the Tomahawk Mastery: Level 3...although I can't promise it won't be frustrating.
Make sure you have several tomahawks in your inventory, and save your game in the Thieves' Landing safehouse. It is from this load game you'll be making your attempt right off the bat (no pun intended). If you attempt and fail, it's advised you quit to the main menu, as opposed to simply loading this save point in the middle of a game (the bats don't seem to respawn unless you quit to main).
Once you load this game, exit the safehouse and immediately turn around so you're facing the door you just exited. Climb up to the top of your safehouse by jumping and grabbing the roof to the left of your door. Face west and you'll see some trees right in front of you (with water off to your left).
Throw a tomahawk into the trees (or, if you're particularly low on tomahawks, shoot a pistol into the trees, pause with Start, and switch to tomahawks from the Weapons menu). This will cause a bunch of bats to fly out of the trees, traveling overhead and to your left. Pivot left and start chucking the 'hawks. If you fail, quit to main, restart, and retry.
You should get it eventually, or soon if you're lucky.
I'll give it a go tonight.