Depends on how long you are in San Juan. The water falls are not close to the city and require an excursion to get there. Many of the itinerary don't get into San Juan until the afternoon and by then its too late to go see them. If you are staying in San Juan and leaving on a cruise that departs from there, then you can go online and book a tour yourself as you may have time.
The distillery can be done and is a standard tour you can do through the ship (or even on your own)
Carnival Cruise Lines:
Fantasy 90, Celebration 95, Victory 05, Conquest 05, Spirit 6/06, Freedom 6/08, Holiday 7/08, Victory 6/09, Valor 9/09, Dream 6/10, Splendor 8/10,Conquest 8/11,Magic 11/11,Triumph 4/12,Spirit 7/12,Freedom 11/12, Triumph 2/13 - The fire cruise, Magic 1/14
NCL Dream October 2006, RCCL Mariner OTS June 2007, Celebrity Silhouette 2013