I have not been to Sea World in a couple years, but in addition to
@momto2js recommendations, I would add the following based on my children's experience (in no particular order): Stingray Lagoon, the Turtle Trek show (depending on the line, but it used to time well with the dolphin show), the Pets Ahoy show, the aquariums in the Journey to Atlantis area and the Manta area, and the Sea Garden area at the back of the park where they often have small animals with handlers.
You will have to plan a little for the shows based on the schedule the day you are there and what your son wants to see (seeing all of them by mid-afternoon may not be possible). I generally agree with
@momto2js top three shows to see (Shamu, Blue Horizon, and Clyde and Seamore). If you have time for a fourth, I would add Pets Ahoy. The other stuff I listed are really just animal viewing opportunities that can be done pretty quickly, based on the time available.
I suggest reviewing recent trip reports with a park map in front of you. There are great reports from
@Gina-Gina-Bo-Bina and others that include lots of pictures to help you decide what to see. Have fun! I distinctly remember taking my son when he was 5, and he loved it!
ETA: You should also look into Shark Encounter, located at the back of the park. You can usually get through it pretty quickly, and it's very cool.