AA dropped EIS some time back and I'm not sure any major airlines now offer frequent flyer options with any of the smaller EIS players. Your SJU options are to fly into SJU then use inter-caribean (re-pay for luggage), cape air ($$$) and so on. Have you looked at the St Thomas/Ferry options and tried freq flyer points to to/from there? You could also mix it up, if to your advantage: SJU one way and STT, the other.