We used STT/ferry for a long time and now exclusively use SJU. More options to get to the mainland, STT airport is not fun going home, and there is a nice DCA to SJU flight in. We also use Island Birds private charter from SJU to EIS as we usually have 9 which is plane max. We fly during weekdays so customs SJU is a breeze.

You will find varried opinions here and there are other threads on this you can search. Here is one

http://www.traveltalkonline.com/ubbthreads.php/ubb/showflat/Number/270102/Searchpage/1/Main/36897/Words/%2Bsju+%2Bvs+%2Bstt/Search/true/re-decisions-decisions-bvi-via-stt-or-sju-eis.html#Post270102