Don’t we have the answer? Neither. In the MCU, they don’t even have the excuse of being separated by death or interstellar distance. They chose neither.
They do have the excuse of interstellar distance, at least for Thor. Unless you take that silly short as canon, he was in Asgard at the time.
And Banner has been trying so hard to stay out of touch, that he might not have even found out about the whole business until after it was over.
Eh. I think you can say that applies to Thor… if he was around and someone brought the issue to him, he’d probably laugh. Keep pressing him, and he’d just get confused and leave to go back to Asgard.
Banner/Hulk’s another issue, though, he’s only not around because he ran away at the end of Age of Ultron and is nowhere to be found. I think Banner would definitely subscribe to Stark’s side. He probably would avoid the showdown at the airstrip, though, not trusting Hulk to hold back.
The Vision is on Stark’s side, and he can actually use the damn thing.
Thor’s a simple god - he doesn’t overthink things. Based on what we’ve seen in the movies, he seems to like Steve more than he likes Tony. That means Team Cap.
But – as MrDibble just reminded us – Thor holds the Vision in unique esteem upon seeing the caped wonder pick up Mjolnir: gives him the benefit of the doubt; figures he’s to be treated as a trusted ally; saw him as a savior in, uh, a vision.
Thor would side with Cap.
In the Avengers, he pointed out a few times that Loki was his brother and thus his responsibility.
Bucky is (for arguments’ sake) Steve’s brother and thus Thor would understand how Cap would want to solve the issue himself.
Banner, I honestly don’t know. I think he wouldn’t like the government trying to control things, but his rational mind would agree that perhaps it is the best path to finding a way to control the monster. Also, Widow and Stark are his buddies. Yet I think he’d be the most critical of all…
As for the ‘factual’ where they were. I think it was hinted that Thor 3 takes place during the Civil War? It’ll feature Hulk & Thor off world.
All that is true, but I still think that Steve is his closest friend among all of the Avengers, and in Thor’s Viking mind, that’s what’s most important.
Besides, he’s already accepted Cap as team leader, which must not have been very easy for a prince of Asgard. Do you really think he’d follow Stark’s orders? As far as Thor is concerned, there are only two options: Team Cap, or Team Thor.
Let’s not forget that Team Thor has Darryl. “Big D” could easily be the deciding factor, what with his vacuuming skills and his abilty to craft electronic letters. 
Iron Man shot Hulk into space, so no way he sides with puny Tin Man if he’d come back in time.
And Thor was dead, but had he come back in time, I bet he’d be none too pleased with Tony’s fake Thor.
Thor is dead? I can’t remember.
Odin sleeping all the time bugs me. When Thor takes the throne is he going to have to sleep all the time? Lazy bastard.