It's not a book, but the CW network has a roughly MG level show, 'Aliens in America', which features a teenage Muslim boy from Pakistan.
To me--a Muslim who grew up in a Catholic-Muslim household--it's funny, balanced, and interesting.
'Does My Head Look Big In This?' is also good, though it appears to have little appeal to non-Muslim MG/YA readers.
'The Glory Garage' (I think that's right) is a collection of stories, sort of YA-Adult crossover.
There are, from time to time, picture books with Muslim characters too, like 'The Librarian of Basra'. I know there are less political ones, too, but I can't think of any titles just now.
At present, I'm planning a story based around a Muslim girl--it's something I missed it out on reading as a child, and would have liked to have.