I took my daughter on a plane for the first time in November, when she was 3 and a half. She still took naps, so I tried my best to get a flight right around naptime. I was worried about the ear thing, and a friend suggested giving her some motrin a little while before boarding the plane. I did, and her ears didn't bother her at all the entire flight. But she was so excited about being on a plane though, that she didn't take a nap until after we got to where we were going.
I'm not sure about the sippy cup thing though. I brought an empty sippy cup with me, and bought a bottled drink once past security. I also brought a small bottle of water for her, which I figured I'd have to throw away - security allowed it through at the departing airport, but didn't allow it at the arriving airport - I thought that was strange.
If it's a long plane ride, be sure to bring lots of things to keep him occupied! No three year old likes to sit in one spot for very long - I brought a portable dvd player and lots of small new toys/coloring books from the dollar store.
Good luck!
~Jessica~