For us, our "must-do's" are -
Chef Mickey's at the Contemporary Resort for breakfast
Cinderella's Royal Table in the MK for breakfast or lunch
Crystal Palace in the MK for lunch
Liberty Tree Tavern in the MK for dinner
We also like Boma at the Animal Kingdom Lodge & 'Ohana at the Poly. This year, we're trying Garden Grill & San Angel Inn at Epcot, Donald's Breakfastasauras at the Animal Kingdom, & Whispering Canyon Cafe at the Wilderness Lodge.
You & your family might also enjoy 1900 Park Fare at the Grand Floridian, California Grill at the Contemporary, Sci-Fi at MGM, Coral Reef at Epcot, Le Cellier at Epcot, & many of the other World Showcase restaurants at Epcot (Marrekesh, Teppanyaki, Biergarten...).
I'm not as familiar w/ the Boardwalk & the DTD restaurants, but your son might like the ESPN Club. Spoodles looks cute for breakfast. The Rainforest Cafe looks cool too - although, it gets mixed reviews.
For counter service, we like Flame Tree BBQ in the Animal Kingdom (it's my DH's fav WDW restaurant), Columbia Harbour House in the MK, Toy Story Pizza Planet at MGM, & Earl of Sandwich at DTD. Eating/snacking at the World Showcase counter service restaurants is fun at Epcot.
Do you know what days you'll be at what parks? Will you have the dining plan? Are you staying on-site & looking for some restaurants close to your resort?