2pm out of EIS is fine. Most charter companies require you be off the boat by noon I think. Who are you chartering with? It's probably similar with most of them but might be helpful to know.

We are always with Moorings or Sunsail and we get back to the base a couple of hours before we need to be off the boat. It allows us to take our time getting ready..etc. We usually do most of the packing the night before and just finish up in the morning. Once at the base, we finish up anything left over, return dive tanks..etc shower and often have something to eat before taking a taxi to the airport.

With Cape Air/Jetblue code sharing, you could risk the short layover, just be aware if you did miss the plane, you do risk not getting on the next flight if its sold out - so you could overnight in San Juan (worst case). But you wouldn't lose your ticket, JetBlue would get you on the next available flight.