Totally agree on avoiding EIS-SJU on the way home. Chances of the EIS to SJU leg being late are high, which means you likely miss your connection. The inconvenience is amplified if your final destination is mid-west or west coast. I prefer to return through STT, ideally NOT on weekend, and if your flight is early afternoon or before, water taxi is the way to go.

If the cost difference isn't too great, we prefer flying in to EIS. Coming from west coast its hard to make the 230 ferry which means you are on the 5:00 ferry and not to your final destination until 7pm or later.