Leaving San Juan at night is absolutely beautiful. I would recommend the starboard (right) side of the ship or at the stern (rear). I have also found that I can usually find more room at the railing on the promenade deck than on the top decks.
If some of your party is coming in early enough to see some of San Juan, they may enjoy touring the old section of San Juan (inside the wall) and also touring the fort El Morro. The fort is a national park and also has a very nice museum inside.