From my understanding, you don't have to be staying at the resort to use the water craft.
If you're staying at the resort, the benefit is being able to charge it to your room.
All the marinas are run by Sammy Duvall Watersports, contracted through Disney, so they don't care if you're staying there or not.
Confirm to make sure, but that's what I was told by one of the marina attendants on my last stay.