Dewey: The Small-Town Library Cat Who Touched the World by Vicki Myron (Libraries and cats are the perfect combination.)
Parnassus on Wheels by Christopher Morley (Not all bookstores need to be stationary.)
I Kill the Mockingbird by Paul Acampora (This sort of takes place in a bookstore. The characters go to as many bookstores as they can and hide copies of To Kill a Mockingbird.)
The Case of the Missing Books by Ian Sansom (Does it count as taking place in a library if all the library books have been stolen?)
The Storied Life of A.J. Fikry by Gabrielle Zevin (I'd love to visit A.J.'s little bookstore.)
84, Charing Cross Road by Helene Hanff (Bookstores in London - even better!)
Sixpence House: Lost in a Town of Books by Paul Collins (This isn't just one bookstore. This is a town full of bookstores!)
Escape from Mr. Lemoncello's Library by Chris Grabenstein (This is the coolest library ever!)