Taken from this post:
1) Dive into the water, either from the rooftop directly (move along
the roof to the right of the mission start-point) or work your way
down to ground level
2) Swim to the other side of the boat- DO NOT get too close to the
boat until you are round the other side
3) Climb up the hull to the right-hand side section of rigging just
until you are able to grab the top railing
4) Shimmy across until you are towards the back of the boat, just
behind the 2 guards that are over-looking your target
5) Wait until all patrolling guards are away from you (you can try and
ledge assassinate some, one of my friends said this worked however it
did not work for me)
6) Climb up and immediately drop onto the deck
7) IMMEDIATELY drop a smoke bomb- you should have time to do this just
before you are spotted
8) Run past all guards, jump onto the rail above your target, and air
assassinate him... DONE!
Alternatively, as user bobbyrk puts it:
The way I did it, was first to swim around the front side of the boat,
away from the dock. Climb up the side of the boat, and when the first
guard gets to the back left corner of the boat, pull him over the
edge.
You don't have enough time to slide over and pull the second rear
guard overboard, so don't bother trying. The guard on the dock will
return, you have to be about three meters from the rear of the boat
for him to not see you when he reaches his stopping point at the end
of the dock. When he turns and walks away, monkey over to the back of
the boat, take out the second rear guard, then jump to the dock, and
use the gun to take out the dock guard. That'll draw the attention of
the brutes and the guards at the front of the boat if you time it
right.
Get back in the water, and climb over to the left front side of the
boat, near the forward stopping point of the patrolling guard on that
side. When he gets there, pull him overboard. Repeat that process for
the other patrolling guard. Don't bother with the two guards in the
front end of the boat.
Circle to the back end of the boat, climb up and walk slowly up behind
the two guards in front of the wheel. Walk between them so you stab
both at once, and you'll be free to take the target out.