Another Comment on the Books Canonicity
This link is to a Steam Post Scott made about The Silver Eyes becoming a New York Times Bestseller. He notes that "while it's true that it doesn't follow the events of the games 100%, it's still good to see that most people have accepted it as a part of the FNaF universe."

Is the book canon? AU?
This link is to a Question asked about the Canonicity of The Silver Eyes Book on FNaF 4's Steam Discussions. Scott provided a pretty vague answer based on The FNaF Timeline becoming so dense that he'd need to tell the Story in a different Timeline.