The Hidden Blade Assassin's Creed in Depth

Anonymous Blitz Assassination
Despite appearances, the guards and the target aren't very alert on this level. Run straight for him and air assassinate from the rail.

You'd be spotted right away.
The developers really wanted you to shoot Marco from the shore. They were even willing to lie a little to get you to assassinate this way, saying, "You'd be spotted right away" if you attempted to swim to the boat. The fact of the matter is that you can easily jump in the water. They won't spot you.

Hiding in Plain Sight
Really, they just won't spot you. This could have also been done by jumping directly to the rail, just like in the blitz. You just need to keep a some distance from the guards so they don't notice you. Marco is literally blind to you. He relies entirely on his guards to determine your presence.

Stop throwing knives, they tickle!
That's right... He relies entirely on his guards to determine your presence. Marco is injured by throwing knives, but being struck by a knife doesn't trigger his flight. If you climb the rope ladder to the horizontal beam (yard), you can even manage to throw a knife at his face without him running. You may find it easier to lock on to the target as you climb up the rope ladder, instead of trying to lock on when you are high above.

Air Assassinations
You can perform air assassinations from the yard or top, which is the platform that appears similar to a crow's nest. If you assassinate from the top, you must lock on to the target as you climb up the rope ladder. Otherwise, you'll be too far from the target to lock on.

The Sniper
It's fun to snipe the target from the top platform. Despite the loud bang, you are too high up for the guards to see you. After the post-assassination dialog, the guard will look for you... just wait for them to cool down. When they give up their search for you, just dive in the water for an easy escape.

To the best of my knowledge, there is no way to shoot Marco in a fashion that would ordinarily invoke a response from guards, but it fails to do so due to timing the shot with the explosions. This contradicts the advice of Teodora at the beginning of the mission on how to remain undetected.

Stunt Assassination
The stunt assassination leap is quite long, so you need to wait for Marco to end up in a good position. After Marco finishes his speech, he walks around in a simple pattern on the deck. Jump when he turns from the bow.

Air assassination from the other mast
You can also climb the forward mast and yard for air assassinations. Quietly killing the nearby guard by pulling him over is completely optional.

Spring-loaded Air Assassination
You can lock on a target and increase your distance from that target greatly while still maintaining your lock. From a hanging position with your feet planted on a vertical surface, you can then perform an air assassination from extreme heights. This was never intended in the game, so we get a weird animation, where it appears as if Ezio is rapidly accelerated to the target. Hence, "spring-loaded" air assassination. Spring-loaded air assassinations are possible in many different places - it's not limited to just this assassination mission.

Part 2
Here is Part 2 of this article:
http://www.thehiddenblade.com/marco-barbarigo-assassination-variety-pack...