In nonfiction, Into Thin Air by Jon Krakauer.
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Harlan Coben (who also writes for adults) has a great three-part series: Shelter, Second’s Away, and Found. It’s a young adult spinoff of his (adult) Mickey Bolitar series.
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I second the Count of Monte Cristo! I read it in middle school, couldn’t put it down.
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Garth Nix Old Kingdom books. My boys loved Tamora Pierce’s books even though the Alana ones feature a young woman. My older son liked her The Circle Universe Archives - Tamora Pierce books even better. For sci fi - I read a lot of the classic sci fi at that age Heinlein, Asimov’s I, Robot books (Foundation hasn’t aged as well), Dune of course. Anything by Diana Wynne Jones, I loved the series that started with Cart and Cwydder and the Chrestomanci books (which featured wizards in boarding schools long before Harry Potter).
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My S loved the Martian when he was about that age. Project Hail Mary is good too. Great reads if he likes science.
For a completely different type of space travel, Hitchhiker’s Guide to the Galaxy is a household favorite.
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It is a household favorite. My 18 year old is not much of a reader but reads this book every 2 years or so.
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I sometimes used to read what my kids were reading. Enjoyed Enders Game. Also some of the other Olson Scott Card novels, especially Speaker of the Dead
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Nonfiction - a great idea upthread, and reminded me of one of my all-time favorites: Bomb by Steve Sheinkin; many of his other books are also informative and fun reads.
My son also loved the Redwall series when he was about 13. The Harry Potter books are also fun for that age (w/much more info obv than the movies). Son & I also read Dune years ago and enjoyed it a lot!
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In addition to Count of Monte Cristo add in The Three Musketeers, Man in the Iron Mask and Twenty Years After
A Connecticut Yankee in King Arthurs Court
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Fablehaven series by Brandon Mull
Adventurers Wanted series by ML Forman
Robin Hobb’s Farseer trilogy is really good: Assassin’s Apprentice, Royal Assassin, and Assassin’s Quest.
Some of the other books mentioned above might be a bit young-ish for a kid who already tackled Tolkien.
True, but then there are adults who enjoy reading all of these titles. 
Of course, adults don’t generally feel the need to seem more grown up than they really are either.
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As a former teenage boy, great suggestions. You covered a lot of my favorites.
I’d add Patricia Wrede’s books (the Enchanted Forest series and Mairelon duology), virtually everything by Lloyd Alexander (especially the Prydain and Vesper Holly series), and the Dragon of the Lost Sea books by Laurence Yep.
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The Percy Jackson books by Rick Riordan
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Wow, these are some great suggestions. I have a list now and have checked with my daughter (his mom) to make sure he doesn’t have/read some of them. I love to send books every so often as who doesn’t want a new book? ( I know-my husband). I recognize many of these but there are some I don’t recognize. I knew CC would not let me down.
Not a lot of these suggestions like Redwall are popular with adults. I agree with @billythegoldfish that most of these suggestions seem like elementary school age books Redwall, Ranger’s Apprentice, Brotherband, the Lion the Witch and the Wardrobe, etc, are all books that are found in the children’s section, not the young adult/teen section, at my local library.
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Nonfiction The Boys In The Boat by Daniel James Brown - really exciting writing of a true story of UW crew team
He will not be able to put it down
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Forgot to mention there is a young readers version but I think the original would be fine.
My kids also liked “From the Mixed-Up Files of Mrs. Basil E. Frankweiler,” “The Westing Game,” and “Julie and the Wolves,” as well as “ Riffles for Waite.”
Those are all quick and easy reads but books my kids returned to multiple times.