Pirates of Barracuda Bay 21322 — are there instructions to build it as a seaworthy ship directly?
LEGO provide instructions for the alternative build.

However these are given as an 'alteration' of the existing set rather than steps from scratch, this means you must create the official model first before making the changes.

The steps to convert the ship are on pages 412 to 450 of the instructions. Digital PDF instructions can be found on the LEGO site but I have also uploaded an image gallery of all the steps.
It is entirely possible to simply skip building the island stages as you will not need most of those parts in the conversion and the majority of the ship will be built.
My advice would be to follow the instructions ignoring those stages and simply assemble the three parts of the ship, making any alterations necessary using the instructions in the later half.