Just to be different I'll say San Cristobal. You have already seen the harbor if you were on deck when you come into port and you get great photos of El Morro from the ship.
San Cristobal is higher and gives a fabulous 360 degree view of the harbor, Ocean, City etc. There is an interesting 15 minute movie and plenty to explore.
Now that you've heard two different answers I hope you are not thoroughly confused.
SanCristobal is also within walking distance of the pier.
Take the free trolley downtown to El Morro. The views are fantastic and the fort is huge. There's so much to see and the ride there and the tour is free! The trolley runs by every half hour for your return. This is a must see!
I've been to both, and would El Morro over Cristobal. Better views, great grassy area out front full of families with kites, nice cemetary on the coast, etc. Both are very nice, but I give the node to El Morro
You can get on the free trolley on the side street near the Bus Depot across from the ship's piers. Or, walk to the Pink Information building for a great walking pocket map. I believe the trolley stops near there. It is only a 5 minute walk from the piers along the waterfront. Take the trolley all the way up to El Morro and walk back down hill from their. Plan to get off ship as soon as it is cleared and you will have plenty of time to do a great walking tour of Old San Juan. Don't miss a stop at El Convento for a cool drink in their courtyard.