3 hours sounds like an awfully long time, but by the time you deplane, hit the restroom, maybe grab a bite to eat or something to drink, and do the shuttle ride, it will probably be almost time to start boarding your 2nd flight.
I think you'll be fine with your plan. Maybe a couple of coloring books like someone suggested, just in case, but when DS was little, we used to take turns just walking around the terminal with him, since he'll be sitting for the flight.