“Every one of the books is..” is correct out of those two.
“Everyone” means all of the people in a group. You separate the words every and one when you want to emphasize each individual. Ex: “I want to thank everyone for coming” vs. “I want to thank every one of you for coming”
Because everyone = everybody or every person, I would not use it to talk about a group of objects, such as books.
“Every one of the books is..” or “All of the books are..” would both be correct.