Do check with your car rental agency about taking the car on the ferry to St. John. When we did this a couple years back, Hertz would not let their cars go to St. John, while Budget would for example. Car rentals are a bit pricier on St. John, and you also have the advantage of loading up on supplies in St. Thomas and taking them with you in the car. So overall, including not having to take a taxi from the St. Thomas airport to the ferry terminal and to walk from the ferry terminal in St. John to the car rental agencies, it made sense to us to rent from Budget in St. Thomas and take the car to St. John.
However, I don't know that you absolutely need a car at the Marriott on St. Thomas. They have a water taxi into town, and it is a nice self-contained resort with everything you would need, but if you want to get around St. Thomas, taxi fares would quickly add up to the daily cost of a rental car.
St. John is small and doesn't take too long to go from one end of the island to the other. The east end where the Concordia resort is tends to be much quieter and there are beautiful beaches close by also. Fewer restaurants, but there are some. Concordia is an eco-resort and it is really a different category of resort than Caneel Bay. If you are staying at the Marriott on St. Thomas, that is closer in resort feel to Caneel Bay than the Concordia. There are plenty of vacation rentals by owner also all over St. John.