Legoland might also be a good option.
If he's into Marvel superheroes at all (Spiderman, X-Men, etc) and at least 40 inches - Islands of Adventure would be a great choice for Marvel Superhero Island. I've seen kids spend the entire day just in that last alone to do the rides, meet all the superheroes and villains, and get your picture taken with Spiderman to be on the cover of the 'newspaper'. Plus there's the whole rest of the park ...
If he likes whales, dolphins, and the rest SeaWorld is always fun and usually less crowded than the other parks.
Disney parks might kind of ruin the point of a Disney cruise but Magic Kingdom is fun for all ages.
You said 3 days - arriving, middle full day, and departing? If so, maybe only do one park in the full middle day and do other fun things on the short days. (This would also save some money if that's a concern).
It really depends on what he likes/how tall he is/how much you are willing to spend. Whatever you decide, I hope you have fun!
Personally, I think visiting the Disney parks is a perfect compliment to a Disney cruise... it keeps you "in the magic" for a few more days. I recommend you visit two days at the Magic Kingdom (at 40" the kid can ride everything but Space Mountain which is 44") and one day at SeaWorld or Legoland (or DHS if you prefer to keep it all Disney).
Who are his favorite characters? Disney's Hollywood Studios is a good fill in for Universal Studios. Lots of shows and really only a couple of rides he will be short on. Especially if he likes Mickey Mouse Clubhouse, that might be an option.
The Darkhorse in this selection would be Animal Kingdom. I feel that it is underrated as a family park. Everybody loves animals and its a park that everybody can enjoy on their own level.
I know what park you shouldn't take him too: EPCOT. Don't get me wrong, EPCOT is one of my favorite parks, but the adults will have much more fun than the kids (especially young kids)
We brought our oldest daughter there when she was 4 (almost 5). Everything at Seuss Landing is a must and an absolute thrill to a little one. ESPECIALLY if they love the books like my daughter does. She met the cat in the hat there. I have a nice picture of him and my daughter hanging up on the wall near her bed. My daughter wanted to do everything twice there. And we did. The lines are never long.
At Harry Potter, my daughter went on Flight of the Hippogriff twice in a row (the second time they reserved the front seat for her because she was back in line so quickly). She then walked through Hogwarts with my wife and I (we did a child swap). She has no idea there was a ride in there, she was just blown away that she went to Hogwarts. The child swap area has large TVs that play the movies. So she was just entranced by that until it was time to leave. Then she got to get some butter beer and then buy candy at Honeydukes.
We then went to Jurassic Park where she went on Pterandon Flyers (she didn't mind the loooooong line). Then we all explored the heights of the Camp Jurassic area which is pretty amazing and then went below to the Discovery Center where there is so much for a kid to look at.
From there it was over to Toon Lagoon where she got to play in the Me Ship, the Olive area. It was hot, so she was happy to get soaked. Then over to Marvel for Spiderman and Storm. I was nervous my daughter would be terrified on Spiderman. After she got off she yelled, "oh yeah!" and pumped her fist in the air. It was hilarious.
From there, we went to what is left of the Lost Continent. Saw the Sinbad stunt show and then entranced by the Mystic fountain and then made our way to Poseidon's Fury. That was the closest my daughter came to being scared her entire time there.
Anyway, just wanted to explain that a five year old can have a blast at Islands of Adventure. Sure they can't go on the big kid rides, but there is still PLENTY for them to do and it was also give them a lot to look forward to on the next trip when they are bigger. :)
Walt Disney World
Tokyo Disney Resort