Reese flew home with me from California....7 hours total....4 the first leg then 3...and until the stewardess asked to see him no one even knew he was on the plane. I'd suggest the medium carrier. Place a pee pad inside...although to be honest...Reese went before we got on the plane and didn't go again until we landed. I gave him some nytrical before we boarded, had a small bag of kibble, and a travel water bottle.
Enjoy your new baby....you'll get lots of awww's in the airport.