We have done both, but 95% of the time go through SJU to EIS. We are on the east end, so it would take half a day to get here using the ferry, plus the taxi would eat up any savings.

For us, STT only works if we charter a plane to EIS, or if we can connect using Cape Air. The latter can work very well if you are booking last minute.

The other big factor is your final day: you have to allow lots of time going through STT, especially on the weekend. The lines at Customs and Immigration can be long, as well as the airport lines, given that most flights leave about the same time.

San Juan is not perfect, but we, and many of our neighbors, have taken to flying in late the day before, staying at the airport hotel and catching the early Seaborne flight. This saves money and makes for a much more restful arrival.