According to FlightAware for SJU to EIS:
Monday (6/13) - Cape Air was 6 for 6 (no cancellations)
Tuesday - Cape Air has completed 2 flights, cancelled 2 and the 5:00 flight is scheduled.

InterCaribbean has been averaging 2 for 3 for the last couple months....by my casual observation.

We came down in May (on IC and Silver) and didn't have any issues. Had some luck on our side, I guess. But, we had some flexibility so weren't too stressed about it.

I would definitely ferry (or water taxi) to STT for the return trip home....less chance screwing up your connecting flight(s)