There are several rental car companies on St John, and I'm happy to make recommendations.
The VI Tourism Office has a partial list of Rental Car Companies on St John.
After flying into St Thomas, you'll either rent a car at or near the airport or take a taxi to the Red Hook passenger ferry terminal and rent a car on St John.
There are pros and cons to both, which I'm happy to discuss with you.
The VI Toursim Office has information about car and passenger ferries.