This was in early June. We did this twice.
We waited at the bottom of the ramp of Innoventions around 10:30-ish. We were first in line both times. My son loves the Iron Man interactive exhibit, so both times, he did that first. After Iron Man, we went straight to either Thor or Captain America. Both times, we waited maybe 10 minutes or less.
Like other posters said, for Thor, you have to go into a separate room as a group and then from there to the chamber where Thor is.
If you don't want to do the Iron Man interactive and you are in line by 10:45, you shouldn't have more than a 5 minute wait for either Thor or Capt. There will be a line and you probably won't be first, but you won't have a very long wait either.
In early June, by 11:00, before they let us all in, the line circled all the way around that little hub, past Space Mtn, the Star Wars store, the fruit and veggie stand, and started making its way down to the open air dining area.
(also, if you have photopass, the Iron Man interactive exhibit will take pics of you wearing your Iron Man armor - cool stuff!)
HTH!
