It has been $1 per bag as long as I can remember. Actually, I'm surprised it hasn't gone up in the last 13 years.
I don't consider $16 for the cab fare from the airport to the pier plus $2 for our 2 bags to be all that bad. That's about $18 for a roughly 13 miles trip. I pay $23 to get from our house to Dulles Airport and it's only about 8 miles! From the Ft. Lauderdale airport to the pier, which is only about 4.5 miles, is $12. So when you look at cost versus mileage, San Juan is not such a bad deal at all.
Plus, while we're standing in line at the Puerto Rico airport, we ask people if they're going to the same ship we are and inevitably we always find someone so we can share a van. Price then becomes $20 for 4 people with a total of 4 bags. At $5 per person, that's a deal! And coming back is easier because almost everyone is heading to the airport so it's not a problem finding someone to share a taxi. In fact, I can't ever remember a time we didn't share a taxi to/from the pier.