I lived in San Juan and we used that Ferry on occasion. (I think it cost a dime back then.) You can catch the ferry, right next to the cruise ship piers. However crossing the bay to Catano takes you to an area of San Juan that is a little economically depressed, so be careful.
I recommend getting a group to go, not just a couple and I think there are often taxis right there. From there it is about a 10 minutes drive to Bacardi.
Make sure you check tour times before venturing over.