I agree with Donna that a vist to El Morro is a must see in San Juan. You can wander around old San Juan at your own leisurly pace, its not a difficult walk at all. You might consider a tour up to the rain forest for something interesting and different.
When we were in San Juan on the Carnival Triumph in Feb we didn't dock until around 5pm so the El Morro fort was closed unfortunately. I would have loved to go there. Entering the harbor we got great pics of it though as you can almost reach out and touch it!
We did the old san juan/new san juan bus tour the ship offered. It was nice as it was the evening so we didn't want to be out on the streets in the dark but we got to see some of the old city and the new city plus shop along the way. There wasn't too much walking except to shop.
Don't know if you already went on your cruise, but if you can go to the El San Juan Hotel and Casino, in Isla Verde, it is a beautiful site to be in that lobby and casino. They have imported wood and marble from all over the world to put it together.
We are on Carnival Victory leaving Dec 28. We arrive at San Juan at 5:00 pm too so assume we won't be able to do too much. How much was the old san juan/new san juan bus tour you booked from the ship? We have 5 in our family so am looking to save as much $$$ as possible. Is there anything else to do in San Juan after 5:00 pm?