I'm generally averse to recommendation lists, as every city, especially Tokyo, has been extensively documented and mapped.
However, there's one longtime favourite that I always recommend to visitors: Tsutaya Books in Daikanyama, also known as T-Site.
T-Site is not only a design pilgrimage, with Klein Dytham's handsome three-pavilion architecture, but it also makes a strong case for what bookshops should be.
The space itself is inviting, with generous proportions and sight lines that encourage exploration.
An afternoon here doesn’t require purchasing anything.
Author's summary: T-Site is a must-visit destination in Tokyo.