How can I remove a PDF in iTunes?
Can you not select the book and use Command ⌘ + Delete ⌫?
You'll be presented with a choice to delete the book from the library, or move it to the trash:

You'll probably want to move it to the trash, unless it's a PDF that you don't have somewhere else. Also, make sure that you are going to the books tab on your computer, not managing the books on your device.
Here:

Not here: