When sailed to San Juan a few years ago on the Liberty arrived late in the day and I felt as though we missed out on some things, because it was dark out. Fortunately it was a full moon so we still went up to El Morro and explored.
***I had to edit this because I got a little mixed up on how we made it to San Juan the last time***
The next time we went there, we were on Carnival Triumph October 3rd, 2007 and it was during daylight hours, arrival 7:00 a.m. and departure 3:30 p.m., which I thought was great, but it was so bloody hot, we were miserable and ended going up to the ship early. I think if it had been in January it would have been much more enjoyable.
So I really don't know which is better.