Hi Kristy!
I think that a lot of people feel that Disney is all about Princesses and boys get left out. I have two boys and I'm hEAR to tell you, there are lots of special things for boys too! The Pirates League and Jedi Training Academy are both amazing but I don't there is a choice. No really - why choose? Do both! Actually, here's what I'd do because I'm such a huge kid.
If your son is having "his dinner" at T-REX at Downtown Disney, head to the Lego Imagination Center afterwards. Its just next door and all of your kids will love playing there and seeing all the awesome statutes they've created. You could also visit RIDEMAKERZ (build your own radio-controlled car) located in the Team Mickey Athletic Club.
For your son's special experience, take him to
The Pirates League in the Magic Kingdom. If it fits into your afternoon schedule that day, be sure to bring him back to Adventureland that afternoon for the Parade of Pirates. Its typically held around 4 p.m. but they will confirm the time for you at The Pirates League.
Jedi Training Academy is out of this world fun for kids ages 4 - 12. This experience is included in the price of admission at Disney's Hollywood Studios so I'd make it a must do for any of your kids in that age range. I recently answered a question for a guest with
details of where and how to sign up for Jedi Training Academy that I think you'll find helpful.
If your son is into the great outdoors, he may enjoy the
Fort Wilderness Archery Experience. I'm out of room for this answer but please let us know if you need other suggestions.
Wishing you minnie magical memories :-) Allison