Where are the Overdue Books?

There are definitely some outside of the library. I've collected a list from a couple of sources... Namely, GamesWiki and Fallout Wikia. The schools scattered throughout the game seem to be a great place to pick up a number of these in one location. You can check these articles for a bit more description on precise location, but combining the lists in their current state yields:

• 9 in East Boston Preparatory School
• 8 in Shaw High School
• 6 inside the Boston Public library
• 5 in Suffolk County Charter School
• 4 in Trinity Church
• 4 in D.B. Technical High School
• 4 in Collegiate Administration Building
• 4 in Sandy Coves Convalescence Home
• 3 in a Pulowski Preservation Shelter, South end of Trinity Plaza
• 3 in Natick Police Department
• 2 in subway station West of Hangman's Alley
• 2 in the Kendall Hospital
• 2 in the ArcJet Systems building
• 1 in the laundromat in Lexington
• 1 in the Walden Pond gift shop
• 1 in USAF Satellite Station Olivia
• 1 in Faneuil Hall
• 1 in a trader's shack west of Ranger cabin
• 1 in Quincy Police Department
• 1 in Mass Fusion building
• 1 as quest reward for Public Knowledge, given by Daisy in Goodneighbor
• 1 in Covenant
• 1 in the subway tunnels during the quest The Big Dig
• 1 in Saugus Ironworks
• 1 in Harbormaster Hotel
• 1 in Lexington Apartments
• 1 in Boston Mayoral Shelter
• 1 in Pulowski Preservation Shelter in front of D.B. Technical High School
• 1 in Bethany's Shack, NW of ArcJet Systems
• 1 in Parkview Apartments
• 1 in Milton General Hospital
• 1 in Parsons State Insane Asylum
• 1 in Museum of Witchcraft
• 1 in Plumber's Secret, Cambridge

Overdue books may also be for sale at some vendors, including general stores in settlements.

Book return tokens can also occasionally be looted. Most notably, the raiders around Revere Beach Station and the loot containers of that area can contain book return tokens, presumably obtained by the raiders from the book return terminal in the nearby building.