I have zero toddler experience, but I enjoy fruit bars on planes. Trader Joes has lots of yummy ones that are pretty soft, and conveniently compact.

Benadryl! No, no - I'm obviously kidding (seriously, don't give him Benadryl)
Oranges/clementines (fun to peel, obviously healthy, and good hydration)
String cheese should be good outside of the refrigerator for that long.
Animal crackers (I would avoid Cheerios et al for the mess-factor alone)

We bring blueberries in a small container (not a bag, as they get crushed!).

Fly at night or nap time if you can so you don't need to entertain for so long.

Lots of food snack choices is part of the key. Buy something at the airport as a special treat - yes, Happy Meals are gross, but bringing one on the plane as a treat for good behavior will pay off in entertainment value.

Bendadyl or Sudafed can help with ear pain that can result from altitude change (binkies will help, too). Mine is prone to ear infections and needed something to assist with congestion.

SSM

Banana chips!