I'm not sure what line you're going on, but depending on the cruise line and airline you're flying, some cruise lines have a luggage valet service. For a fee (I think for Royal Caribbean, for some ports it was $20 plus the bag fees for your airline), they will take your bags to the airport and check them, and provide you with your boarding passes.
Again, I'm not sure if this is offered in San Juan for debarking passengers. It depends on the port, the cruise line, and the airline.
2007 - Majesty of the Seas
2009 - Enchantment of the Seas
2010 - Freedom of the Seas