Non-stop is our priority.
We have flown several times with 3 small children - the younger 2 are twins. They have flown 3 times in 4 years including once when they were only 1 and our ds was 5, then when they were 4 and again this summer when they were 5.
I would book the non-stop flight anyday. That is our criteria for booking a flight. I won't have a layover unless there is no other option.
As somone posted, have a backpack with lots of things to do and also some snacks. We've taken coloring books, plain paper, colors, pencils, cards, small travel games (checkers, magna doodles, etc), disposable cameras to take pictures of each other on the plane, flash cards, small stuffed animals, etc. Having traveled alot with our kids, I have a supply of small toys that work great on a plane or a long car trip and all fit in one small child's backpack and they are thrilled to be responsible for the bag.
This past trip, my dh had his laptop so we saved a disney movie for the last hour of the trip after all the other toys had been played with. They knew they would get to watch the dvd if they did great on the trip and they earned it with some help from us by playing games with them.
There were times when they would ask how much longer, but having an ample supply of games to play and things to do, really helped. To me, this is much easier than having to get off the plane, wait in the airport, get back on the plane again. I'm sure others may feel differently, but non-stop flights have worked best for us when traveling with 3 children.
I'm sure you children will do fine with whatever you decide. Enjoy your trip.