The Monstrumologist series by Rick Yancey is by far the scariest YA horror I have read. I went into it kind of dismissive of the notion of being frightened by spooky creatures in children's books, but by about page 25 something absolutely appalling happened and I knew I was not going to be sleeping any time soon. Three books out so far, one more coming soon.
Long Lankin is another good new scary historical. Keep the windows locked!
And Wuftoom is borderline MG and YA, but it's a really really creepy tale of illness, transformation and losing your humanity. I would recommend it to anyone! Strong stomach recommended.
Scary books that aren't horror: Wintergirls is a contemporary issue book, but I thought it was scarier than any horror novel.