Last cruise out of San Juan earlier this year, we just took a cab. Once you pick up your luggage there is a taxi stand inside that you need to go and get a paper before you get in the taxi line. All the prices are set, they just adjust for the number of pieces of luggage you have, should be around $20 to get you to the port. We found this to be actually much easier and faster than the cruiseline transfers. Depending on traffic, its about a half hour drive to the pier. Once at the pier the driver will hand over your luggage to a porter, tip both the driver and the porter and continue to get to the area where you embark, very simple, enjoy!
Taxis are everywhere. Six of us took a taxi for I think $18. Ofcourse we also tipped for the bags and we had so many it cost us $35 (I think) still reasonable when you divide by 6.
At the luggage terminal there are people going around asking who needs a taxi where and how many people. They take down your name and information- made me feel like I was at Cracker barrel waiting for a table. Within 15 minutes we were called that there was a taxi for us and because there were six of us we got a van instead of a minivan. With all our luggage we were still crammed in.