The taxi will be cheaper but . . .
When you come out of the AP terminal there will be an ENORMOUS slow moving line & you will be overwhelmed by the heat & humidity. You will get on this line with all of your stuff & wait in an organized manner while you & every other passanger from a minimum of 5 ships (think 5 x 2000 = 10,000 people) waits for a taxi.
Even though it is more expensive, San Juan is the only port I have been to where I would recommend you take the cruise line's shuttle service. Instead of standing in the heat & humidity you will sit & wiat in an air conditioned bus.