Welcome aboard, Maureen! My biggest suggestion is to book at least a few Port Adventures, as Disney will take care of all of the details and ensure that you get to see so much more than you could on your own!
It looks like you'll be visiting the Greek Isles. You are in for a real treat! Santorini was my favorite spot. Be sure to visit the town of Oia. Fira is nice too, but Oia is the best of the two and has so much to offer, not to mention some beautiful views to say the least! When you tender into the port here, there are a few ways to make the trek up the cliff. If you're going with an adventure group, that will be taken care of for you, but if you're heading in on your own, you can either take the cable car up (which I recommend) or try your luck riding a donkey. Let's just say that I gave it a try and wasn't sure I'd live to see the top of the hill! No, it wasn't that bad but there wasn't a place to hold on, so I just stuck my fingers under the donkey's saddle and hoped for the best as we trotted up and later back down the cliff. Whew! What an experience! It made for some great photos and memories though!
Definitely take a Port Adventure in Ephesus. The Best of Ephesus covers about everything, which is a nice way to see the most while you're there. But your son might really enjoy the Archeological Quest in St. John's Basilica and Ephesus tour, where besides experiencing some amazing locales, the family gets to have their own Amazing Race of sorts by being sorted into teams to decipher codes and solve clues. It's history in action! Then, choose one or two of the Greek Isles to explore on a Port Adventure, and perhaps just head out on your own in another of the Greek Isles. You'll want to take a Port Adventure in Malta too, as it's so unique.
Check out my
Disney Cruise Line videos with tips on cruising the Mediterranean, Maureen! Happy planning!