1. What rental co. service St. Thomas and where are they located?
Most of the major car rental agencies have outlets on St. Thomas, but they also are located near the airport. Budget has a location right near the Havensight Port, and they are reasonable. Here is a link to Budget's website on St. Thomas and few other car rental agencies.
http://www.usvi.net/usvi/stthomas/getting_around_stt/car_rental.php
2. Where is the ferry to St. John?
The ferry and car ferry are located at Red Hook in St. Thomas, about a 30 minute or so ride from Charlotte Amalie.
There is a third option, if you're trying to get to St. John with little ones and want them to be safe. Contact one of the taxi services in St. Thomas before you leave. They'll be more than happy to arrange to pick you up and take you to the ferry, though it will be more expensive then just getting a regular taxi, since it will be a private service. You'll need to provide your own car seat, but usually you can request a van, which will have seat belts, to secure a car seat. Then, you can ferry over to St. John and once there, you can then rent your own car from any of the agencies on St. John. It probably will cost you around $150 - $200 this way, but you won't have to worry driving around St. Thomas, and on St. John there are only three roads, so it's not very hard to get lost there!!!!! The two private taxi services we've used with no problem are Dynamic Tours 340-777-7112 and East End Taxi 340-775-6974.
If you decide to rent a car on St. Thomas and drive over to St. John, expect that to cost around $100, for the car rental and car ferry. Here is a website with information about St. John. It has the ferry times, and the car ferry, and the car rental places on St. John. We always rent from Denzil Clynes, and have never had a problem!!!
http://www.stjohnusvi.com/stjohn.html
If anyone needs anything else about St. John, please let me know! That place holds a soft spot in my heart, and I can't wait to get back next year!!!!