On the left boat, swim around to the rear side. There are two patrolling guards; the grenadier and a normal redcoat. The redcoat will stop on the right side (from behind the ship) of the two gaps between the railings. Pull him into the water when the grenadier isn't in sight. Then climb to the rear of the ship (Where the wheel is), and watch the guards. When there is a redcoat standing at the wheel and the grenadier is walking away from the rear of the ship, hop over the railing and hide behind the crates. Corner assassinate the redcoat as he comes around the corner. Stand there and let the grenadier spot you. He'll walk your way; hide behind the crates immediately! As he nears, he'll go wher eyou killed the redcoat. Walk to the other side of the crates (keep the crates between you and the grenadier so he can't see you). With his icon gray, looking for you, climb the boxes and air assassinate him.
Already mentioned. All you have to do is snipe them with your bow and arrows from the mast. Make sure you hold down though so your arrow has a chance to kill them in one shot instead of two. Then all you do is loot the bodies for your bow ammo and repeat it on the next ship.
get a bunch of arrows sneak up the ummm mast? yeah lets go with mast and just snipe everyone before u kill the guy in the kilt...i think its a mast...THE BIGGEST POLE IN THE MIDDLE OF THE SHIP THAT HOLDS THE BIGGEST FLAG.