Unlike Suze Reese, I actually felt like this wasn't all that hard. But then, if you include Harry Potter, it means you're not really being that strict about what's YA. But if we're saying YA-age male protagonists, Christopher Chant and Miles Vorkosigan are my (current) top 2!
And Miles! Midgety and with cracking bones, he occasionally has bouts of self-doubt, but not often. He knows he's a genius. And when he's in a clinch, he's the smartest dude ever!
So basically, I have the opposite preferences about my male protags. I don't want humble, I want cocky. I want super smart. I want confidence.
Basically, I want the same thing in my male protagonists as in my female ones. I want people who know who they are, who are light on the angst, and as smart as hell.
You know, the same sort of things I like in my friends.