Querulous
Add this word to your brain-banks, guys, because it describes the tone of the book perfectly. Whiny, petulant, discontented, plaintive—all fun words that would work, but say it with us: querulous. Doesn't it sound like some kind of Harry Potter spell?
This is not to say that the book itself is a bummer to read—it's actually super fun—but since the story is told through the thoughts and feelings of Thomas, these are the prevalent emotions being conveyed. For example, there is a lot of this:
Thomas looked over at Newt, hoping for help. Everything inside him churned and hurt; the tears that had yet to come burned his eyes. (2.43)
This tone works with the story, though, because would you want to read this same tale and feel really good about it? Wouldn't it seem a little off if the author had written about this horrible situation and it felt like he should be describing your fifth birthday party? You know, the one with the clowns and the ponies and the awesome balloon animals?