We had friends on board who did the Rainforest Tour in San Juan. The adults said it was a very long and boring bus ride to get there, but that the tour itself was just "ok". Their kids hated it.
I didn't hear one person say anything good about excursions in San Juan. The "Rum Factory Tour" is a big waste of time, no one had good things to say about that tour. We walked around town on our own. There were some areas that didn't seem very welcoming to tourists, so we would just back track and stay on the busy, tourist streets. Most of the restaurants were closed at lunchtime, and the ones that were open weren't very impressive. There were only a couple of restaurants that looked nice, the rest were dives. My recommendatin is to go back to the ship for lunch. You'll save lots of money and have better food.
Most of the stores sold junky souveniers and the nice jewelry stores seemed overpriced compared to St. Thomas jewelry stores. We loved the architecture in San Juan, but that's about it.