I have to agree with Hdawson, there is plenty of time to do both, but get an early start in the morning. If you head over to St. JOhns you will beat all the tours that will end up there. There are also taxi's waiting there to take you back to the ferry and they run every hour, so be sure to allow time for the traveling.
When you get back to St. Thomas if time is running short, you can shop right by the pier in the mall there, same stores as downtown. Have heard that the prices are cheaper downtown, but on our last trip I couldn't tell much of a difference.
Have fun and make sure you get over to St. JOhns, its really paradise, enjoy.