Welcome back, Kim!
There are certain times when guests are able to participate in two different Port Adventures in the same port. When you are able to begin your Online Check-In, it is then that you'll be able to see the exact times of departure for each adventure (some with choices of two times). If the first tour looks like it will be back with plenty of time to spare before the second one begins, go for it! I just caution you that the tour times listed are approximate and can vary based on crowd levels and traffic.
There are a handful of adventures in which three-year olds can participate. Of those specific adventures, my choice would be the El Yunque Rainforest Tour and Hike. Active kids will enjoy exploring the rainforest, and Mom and Dad will love learning all sorts of fascinating information from the guide. What a beautiful place to hike and explore!
If you are considering doing a different Port Adventure with just one adult and your nine-year old, I highly recommend the
Castillo San Cristobal Featuring the Youth Activity (ages 5+). While I haven't had the chance to experience this one myself, I was in the Mediterranean with Disney Cruise Line this summer, where many of their Port Adventures feature a special Youth Activity too. These were by far the best adventures for families and this one is sure to be as well. Disney's Youth Counselors will take the children to create their own clay piece after learning about how the fort was built. During that time, parents have an hour or so of free time to shop and explore San Juan knowing their kids are in good hands, enjoying learning about the culture of San Juan. Not only are you getting a tour of the beautiful town of San Juan, but you're immersing yourself in the true culture of this city and its history!
Happy planning!