There is no special queue for citizens vs. others when you check the boat in from BVI back into USVI. So I don't think there is any additional hassle for you vs. anyone else. The longest I"ve had to spend at C&I coming from BVI back into USVI was in November when we got there right when a ferry pulled up and I think we waited a half hour. From my experience, assuming you have your paperwork ready to go, the checkin is usually on order 10 minutes - hardly a hassle. The hassle you will have coming back through C&I into US proper - either at the STT airport or San Juan will be the same. In other words - I don't think your green card situation really weighs in with the decision.