Ok, hey everyone, my first useless guide here, so i'll get right to it and make it short and sweet for the skim readers. ^.^

Now for the summary, just in case anyone didn't get it, or doesn't want to read too much of what i wrote.

1. Calm waves/weather
2. "fast drive" your ship in the same direction as your target within 150-250m.
3. stop and release your wheel.
4. run and dive off the back of your ship.
5. Swim to target, testing it's reactions to your characters movement, swim away from it diagonally to test if it's turning because of you.
6. Successfully swimming close to said ship of any level depends on you, i capture lvl 60 ships and i'm only to sequence 3.
7. Kill the captain first, always kill the captain first, in case you happen to dive into the water to safety while stealth killing crew.
8. Kill all the crew, or just the captain.
9. Swim to your ship
10. Shoot enemy ship once, now board her.

Congratulations, depending on your choice of killing all the crew and captain, you can now capture the ship, lower your wanted level, repair your ship (no need for repairs right?! ^.^) instantly or after fighting the remaining crew.

Below is a deeper explanation of the summary, in order.

First of all you will need a character, some some stealthy experience, and a ship. Have all that? it's ok i'm sure the animus provided you with all these fun things already.
Now then, you will need "calm weather" waves that are not to tall, not "bashy" so you can easily let go of the wheel by slowing down to a stop and holding the release key (S) for pc users. Is the weather calm? ok head out to any small islands and or the wide open sea.

Your next task is to know how AI pathing works, knowing when your target will turn away, or if it will shoot back. This can also be done while theres ships chasing you, works best with hunter ships at 150m-250m. They refuse to move when you are not at the wheel, easy pickings, and their crew die much faster than other ships.
So you have your target, it's moving fast, maybe you are only comparable to a lvl 2 ship, and your target is a lvl 23 frigate? don't worry you won't be needing your cannons yet. ^.^
Learn your targets path, if you are already sure it's not going to turn a different direction soon, now is your chance, get within 150m's of said enemy, pass it till you are 150m's ahead and facing the same direction as it, quickly slow to a halt (remember the sea is calm right?) and now release the wheel, hold shift, run to the back of the deck, jump off the edge.
Your greatest problem here is knowing how to "read AI" you are not in your ship, but these ships treat you like a giant ship all the same. Swim straight on towards the enemy ship, if it's already too close it will start turning left or right a great deal, you will need to test if its because of you, by swimming away from it while looking at it. These ships react to your movements unless it's changing direction because of it's path, I try to keep an eye on it while swimming far left or right to force it to keep zigzagging toward me, that when i swim away from it at the last moment so it's not threatened by my direction. If all this has gone well, you are now being almost flattened by a huge wooden hull, your job now is to catch onto anything you can grab onto, the ship will come to a full stop.

Congratulations, you are now learned fully on how to realistically capture, board, and assasinate realistically at sea. Now take out the captain, jump overboard back to your ship, shoot it once and board her. Or kill the entire crew (if that isn't too much for you to handle stealth kills from the side) jump into the water, swim back to your ship, shoot her once, board her. In the second instance of wiping out the crew, you still have the option to gain crew a

Hope everyone has fun, to me this is not a glitch or cheat or bug, this is realistically boarding your enemy, any enemy, and allowing you to be a real assasin of the sea, without getting your ship bashed in. This cannot be done during bad weather and high seas, unless you want to swim from a small island or any island, toward a ship that you know will be coming that way soon.

I don't love that the enemy AI ships have bad pathing toward your character, treating you like a gigantic ship, you can't be hurt by by it almost running you down either. But that is the way they made it, i doubt very much that the developers will patch this as they know that changing the AI pathing now, will ruin immersion for all enemy ships in the game, no doubt breaking storyline as well ^.^ So i am happy to write this guide for those of you who love to capture ships your own way, without any consequence patching. :)

Please rate, or not, or give nice or bad comments. I won't be responding as i have covered every last detail about this task for you. :)

Be good to all kitties and dogs in the game, give them a pat once in a while.
Thank you. :)