I was reading adult fiction pretty much exclusively at that age (but I am female). I don't mean to sound like a complete snob, but based on the books you say he's liked, I don't think you need to stick with fantasy/sci-fi, much of which is not great quality in the literary sense. Also, at 13, you may want to consider relaxing worries about adult content? (I mean, I wouldn't give 50 Shades of Gray!) Do you use Goodreads? I think you could find some lists and ideas there.
Hemingway? Orwell? Vonnegut? Sherman Alexie? John Irving? Steinbeck? Catcher in the Rye? Guns, Germs, and Steel? The Immortal Life of Henrietta Lacks? The Kite Runner? To Kill a Mockingbird?
