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 (Bahamas)
2009 - Enchantment of the Seas (Western Caribbean)
2010 - Freedom of the Seas (Western Caribbean)
2013 - Golden Princess (Alaska, roundtrip from Seattle)