I am not familiar with Inter Caribbean. Is there some reason you're not booking straight through to Beef Island? Delta partners with Seaborne, so if you book a flight that connects with one of their flights, you can connect with less than an hour's layover, and your bags will be transferred. (Of course Delta won't let you use miles.)

You do not go through Customs in San Juan on the way down, only on the way back, and for that (plus Agriculture and Security) you should allow at least 2 hours, especially at weekends and holidays.