Go to the tree that is near the bomb house. Angle yourself so that you are not perfectly parallel with the wall. A good angle indicator is the tree root that you are standing near. Slowly mover towards the stone wall and the ledge. Do a sidehop, immediately followed by a jumpslash to get around the stone wall. Now climb on top of the wall, and jump onto the roof.
It is possible to roll clip into the railing of the pirate ship and jump to the loading zone behind the door. First, make sure you have your sword out, and then climb up the ledge and target the wall as you do so. Hold directly left and do a roll clip, then target again and hold directly down. When link begins to fall, jumpslash to get back on the edge of the collision. Then C-up and put the B Button GUI somewhere near the ladder on the pirate ship. Then just do a sidehop and jumpslash and you should be in the loading zone.
Note: This setup only works on the original version of the game, since in the HD version, the loss of notches on the control stick make this particular setup nearly impossible. Another reason this trick is harder in Wind Waker HD is because you need to let go of the control stick immediately after roll clipping in order to prevent yourself from jumping to the ledge above.
By using ledge clipping you are able to skip the entire password and enter the pirate ship directly after arriving at the island. Get one of the pots you can find on the island and walk with it to the ship. Place it on the left rail near the door and make sure it's as far out from the rail and so near the wall as possible without falling of. Use the Deku Leaf to grab the edge near the wall and push left at the frame Link's feet are straightened out. Drop the edge while you are out of bounds on the next frame and glide to the loading zone behind the door.
This is probably the easiest method of doing Password Skip; however, it is slower than the Roll Clip method. First, you need to set the wind to be southeast. Then, climb up onto the top ledge of the Pirate Ship. Now carefully maneuver yourself between the corner of the 2 crossing ledges. If done properly, Link will be partially inside the back wall of the pirate ship. Now let go of the ledge and pull out your leaf. Aim yourself so that you can land on the thin collision that's under the railing on the side of the pirate ship. Now walk carefully along the collision while inside the railing. Once you reach the edge near the side of the pirate ship that has the door, turn around, walk off the collision, and do a jumpslash to land on the very edge of the collision. Go into first person view and turn left a little bit. Do a sidehop and you should land in the loading zone.