What are you looking to do? Sightseeing? Just enjoying the beach? A little of both?
How important is ease of travel?
I'll share our experiences in PR and USVIs.
There are many Marriott properties along the beach in San Juan. Some are a very short cab ride from the airport, others are further out. The new Ritz Carlton is on my future list.
Old San Juan is really lovely if you like historic sites.
The Marriott on St. Thomas has two sections, the upper hotel area on the bluff and the lower, Morning Star units on the beach. Its worth the extra to stay down on the beach.
We stayed at this property on the way to STJ one trip. Are you using points? If so, seriously consider the Ritz Carlton if the difference isn't too great. I did not take this advice and regretted it.
Its an easy trip from the STT airport to either of the St. Thomas properties.