What makes a boy book?

You might want to take a look at Jeanne DuPrau's Books of Ember (City of Ember, People of Sparks. The way I read them, the main character is a girl, but her best buddy is a boy and he plays nearly an equal role. At the end of People of Sparks the characters are split up for a time and the author tells each story in alternating chapters, so each character alternates as the MC. Both kids are strong and brave; there is no "romance" to speak of at all. It's the perfect book for boys and girls who haven't hit the "boy-crazy" stage yet and don't filter everything through the boy/girl/crush filter. I don't think you need to change your MC. You might want to introduce a lesser male protagonist, but I think those books will at least give you an example of successful books that can appeal to boys and/or girls and might help you as you put together your query.

I, personally, feel that what makes a 'Boy' book a 'Boy' book is what's on the cover. If you look at the covers for Hunger Games and Divergent, they've used symbols rather than a picture of the MC. Why, because a boy would be more likely to crack the book open and be captured by the prose.

If I tore the covers off of the October Daye Series or The Marla Mason Series, I think the same thing would happen.

Librarians

At some point in my research, I found that the best people to ask what books appeal to boys are the librarians. Unfortunately, I'm not a librarian, but I learned this from them - fantasy, Science fiction, adventure and action are what make boys boys.