I'd say the best bet is figuring out who voices Mysterion and comparing that with who voices the others.
I'd safely say that it isn't Kyle (because they speak to eachother), Wendy (Mysterion is male (his underwear and voice)) and it isn't Stan (his dialect with Kyle is more formal than Stan and Kyle's conversations have ever been, lacking the colloquial "dude" and claiming Kyle is the smartest kid in class, not the smartest kid he knows, hinting to the fact that it is a classmate that isn't close to Kyle)
Not Kenny, they tend to avoid showing his face and he couldn't afford the costume. Also, in the movie, when they first showed Kenny's face, his closest friends barely recognized him. Of course, the entire town wouldn't recognize him if this was the case.
Not Craig. He has a very distinct nasally voice and speaks in short sarcastic anecdotes. Also, in the episode in Peru, he completely bemoans the adventures the South Park kids find themselves in. Why would he then get into a costume and fight crime by night?
The clue with Clyde falling asleep is iffy because it happens before Mysterion is introduced. However, this doesn't mean that he hadn't spent time as a vigilante the night before and just hadn't met The Coon.
I think the creators did not intend for Mysterion to be anyone in particular, but gun to my head I'd choose Clyde.