Do you have to change planes?
Either one is going to mess with their routine, so when I'm faced with messing with either or both of my children's routines I look back and try to choose the lesser of the two evils for lack of a better term.
I guess you have to look back at the times you have had to vary their schedule, and conclude if you feel they will handle better going to bed later than usual or getting up earlier than usual? I would lean towards the early flight because the one concern I have reading your post is I see a possibility they could fall asleep during the trip and end up waking during the time they would normally be in their heaviest sleep. That might not be pretty for you.
My daughter flew 4 times between age 18 mo and 4 years. My son has flown 3 times, age 10 months, 21 months and 2.5 years old. We have generally done early mornings, especially when my daughter was my only child and little. My daughter was the one who was on the 6am and 7am flights with us. She was pretty transferrable. Once she didnt wake up until we were at the gate. Now, Im on my own with them and shes older so I try to schedule outbound flights between 8am and 10am usually and returning flights between 2 and 4.
I did one late afternoon flight. It was my daughters fall break and we flew out the last school day she had before it. I got her an hour before dismissal and our flight was at 5:20. The only problem with that was my son, also known as Mr. Regular, usually uses the bathroom between the hours of 5 and 7pm.
All that being said, we are less than a 2 hour flight from Orlando and that is where we have gone most of the time. We have also had non-stop flights since I had my son. When we took that late flight, we landed by 7:15 and we were in our hotel room by 8:30, which is about 30 minutes past his bedtime then. I put him down just before 8, so it was kind of stretching it for my son, by the time we got settled and I got him down, but he isnt generally going to get upset about going to bed an hour late, but if hed gone to sleep for what his body thought was "for the night" on the plane and woken up in transition&YIKES!