Late to the party here, but I too am LOVING this game. It's really spectacular. One of my favorite things to do is to try takedowns. I've been using my skills mostly to get different takedown types, which I fully intend to try out. Sadly, I've only had an opportunity to really try one or two.
One of the most fun things I've found is taking out pirate bases. My preferred technique is long-range sniping with the silenced M700 and the high powered scope. Once oyu have this, with a little patience, you can really wreak havoc on an outpost. I usually try to get to high ground overlooking the outpost, then use the camera to tag everyone I can, and then just start picking them off.
One of the most satisfying rounds of this was when I freaked out some of the guys with molotovs, and they managed to set bascially half a mountainside on fire. the fire just traveled with the wind and blew up the side of the mountain FAR longer than I'd have expected. It was brilliant. You really get the sense of how DANGEROUS fire can be if you're not careful with it, and it's made me wary of relying too much on fire-based attacks (molotovs, flamethrower, fire arrows, exploding fuel drums, etc.) You could end up with a wildfire burning up towards you if you aren't careful!
As far as doing the boat mission, your best bet is to probably go take on enough radio towers to get the sniper rifle or at least the bow. Then take a lot of time to tag everyone you can, and start picking them off silently. I wouldn't try doing stealth takedowns, since there's far too much open ground there, even with all the crates and such. It's a tough mission, though, no question.
