Welcome aboard, Jeremy! San Juan is one of Disney's newest ports, and there is so much to explore there!
While I have visited San Juan, I haven't taken either of those Port Adventures, but I can say for sure that just going into the rainforest on either of those hikes will be a real treat. If you haven't done so already, you can read about them both on the
Port Adventures page of Disney Cruise Line's website. Be sure to select San Juan as your port.
The El Yunque Rainforest Tour and Hike (to Coca Falls) is about half the cost and not quite as strenuous as the Rainforest Nature Walk and Waterfall Adventure (to La Mina Falls.) For your family with a 6 and 9 year old, I'd most likely choose the El Yunque (Coca Falls) tour. I asked my friend who lives in Puerto Rico and is also on the Disney Parks Moms Panel, and he said that both are wonderful tours, but his family's favorite is La Mina Falls, though only because it is tradition for them. Both offer a unique experience, so you really can't go wrong with either.
I also hope you'll have some time right at the port area to explore Old San Juan, as it's one of my favorite areas in Puerto Rico. I loved my visit there and I am sure you will too.
Have a great cruise!