Captain Hook's Pirate Ship anchored in Skull Rock Cove --- the best!
It was located where Dumbo the Flying Elephant is now.
An obvious location for its return (similar to, but I imagine even better than the current Disneyland Paris version!) would be where the Motor Boat Cruise used to reside (and let the Imagineers deal with the Monorail track somehow!).
Looking at a Google satellite map, there's plenty of room for the Ship, Skull Rock, the Lagoon, the obligatory merchandise store, and maybe a "Chicken of the Sea" sandwich shop --- or even a restaurant . . . !