My two cents...

Typically I would say that you should use your Delta miles to fly in and out of San Juan and take a flight on either Silver/Seaborne, Cape Air, InterCaribbean or one of the many choices. In January we got our InterCaribbean flight for $100 each way. Yes, it's risky as some of their flights have been cancelled but we go into with our eyes wide open and realize that there could be a glitch on that end. Usually when they cancel a flight you can get on the next one. We are almost always on the last flight of the day and haven't had a problem with that flight not going. That being said, I do think the ferries will be up and running by June. Just make sure you aren't flying out of St. Thomas on a Saturday and if you are make sure you leave yourself with lots of time or have Global Entry. I just flew out of St. Thomas last Saturday and the line was crazy! I heard some people saying that they had waited in line for over 3 hours. I have Global Entry so I went to the entry point for Customs, asked a security officer where the Global Entry line was and she escorted me to the front of the line. TSA precheck was also open that day so I probably spent no more than 30 minutes going through both Customs and TSA.

As far as time spent in quarantine...definitely see if they can extend to 4 days. Quarantining on the boat was not a hardship and it was nice to have 9 solid days to explore! You can read my trip report to get ideas of what we did.