I have an Action Replay and I got some cool stuff on the island where after..

Your action replay may be screwing up with the game I suggest just saving and pushing reset (well I did and I beat the game twice!)

I don't know if having action replay has anything to do with you being able to get on your boat. You should be able to walk up right next to it on it's left or right side and hit "A" to get in. Unless there is something that the boat told you to do while you were on that island, you should be able to get on him. Get infront of him and hit "A" to talk to him and see what he tells you.

Don't use any of those cheats until after getting the wind waker. Otherwise the game will not work correctly.
Im taking a wild guess that the boat tries to tell you the same thing over and over again and not allowing you to go onboard.

I know how you feel I did the same thing (kinda)
I used action reaplay to beat alot of the game and it worked fine but thene it broke and now half the people on every island are gone.
The only advise I can offer is to use it again because I borowed a friends and whene I put it in and tunned on some cheats it worked fine all the poep[le were back.
But you should just reset the game if you are not to far because I don't think it will work propperly again hope I helped =)

That's what you get for cheating.
Just delete that file and remove it from your action replay list.
Now because I feel like doing Saw imitations:
"You wanna play a game?"

You also have to rescue tingle from jail and get a sea chart.