Is this for Accelerated Reader or some similar program? This is tricky, because most books nowadays are not written above a 7th-grade reading level, no matter what age group they're meant to entice, even adults. For that reason, I would stick with classics. They're usually written at a higher level and they're generally "clean." I did a search in my middle school library catalog (I'm a middle school librarian) and found: Great Expectations, The Phantom of the Opera, War and Peace, 1984, and Dr. Jekyll and Mr. Hyde. I'm sure a more extensive search could produce many, many more such titles... If he doesn't have to read just fiction, there are TONS of nonfiction that is written on the higher AR levels that would be perfectly appropriate content-wise for a 6th grader to read.

I'd recommend John Green's Papertowns or Abundance of Katherines (just not his title Looking for Alaska!). He's a great contemporary author with a sense of humor and usually incorporates history and geography into his novels in unique ways. There is also Jerry Spinelli's Stargirl, which is really popular. There are also Scott Westerfeld's Uglies series and So Yesterday, all interesting novels that tackle social norms and politics that doesn't go to inappropriate places and manages not to be labeled "dull" or "uncool."