If the plane is less than crowded, find an empty row and just let him walk back and forth between the seats. He's going to want to get up and wander because he can.

I'd also advise maybe going against your assumption and getting to the airport a little early to give him some time in the airport to run around. Find an empty gate and just let him run/waddle up and down the aisle. See if he'll get it out of his system there.

The iPad will definitely work. Any games or videos on your phone will work. Mostly you're just trying to keep him distracted as long as possible. Breaking up the flight is both good and bad -- good in that it's a distraction partway through, bad in that the takeoffs and landings are where he's mostly likely to have issues due to pressure.

I assume you're checking your car seat? I wonder if you'd be able to bring it with you and either gate-check it or if it fits in the luggage compartments? Odds are there'll be empty seats, so you may want to keep an eye on the flight and play it by ear in that regard.