im making a "wind waker"/"phantom hourglass" kind of rpg and i need to know how to make the ship be controllable as a character when the character boards the ship.
That's not really a question that has 'an answer', per se. There are many ways it can be done, and how best to go about it will depend on the desired behavior and on how your particular game works.
As with most complex problems though, you should be able to make some headway by breaking it down into smaller parts. For example, regardless of how transfer of control is implemented, you'll need to figure out how you want the controls for the ship to work, and you'll need to implement that control scheme. So, that might be a good place to start; create a scene that just has the ship and the environment in it, and work on getting the control scheme how you want it.
Transferring control from the player to the ship (as controlled by the player) is just a matter of programming; there's really no one answer to the question of 'how to do it'. If you need some ideas though, here's one way you could go about it:
The ship has a boolean variable indicating whether or not it's under the player's control, and the input handling code associated with the ship is only executed when this variable is set to true. When the player enters the ship (e.g. as detected using triggers), the variable is set to true; when the player leaves the ship (however you're handling that), the variable is set to false.
The player has a similar variable, which is always set to the opposite of the ship's variable; so, when the ship is responding to input the player isn't, and vice versa.
There are plenty of other ways to do it, of course. Also, an actual implementation will most likely be more complicated than what I described above (quite often, the hard part with stuff like this isn't getting it to work, but rather making it polished).