Tsutaya's Daikanyama T-Site complex is the best bookstore I have ever been to. And I say this as someone who can actually read a very small portion of the books on offer.
Tokyo's Klein Dytham Architecture won an award at the World Architecture Festival for their work on Daikanyama T-Site, which opened in 2011.
Described as a 'third place', that comfortable spot between work and home, the store puts to bed the idea that print is dead. Print is far from dead, it even just got a fancy new home. Writing is still very much in vogue here too- a visit to the pen cave is a transformative experience. You can have your chosen one engraved, just keep an eye on the price. There are some very, very premium pens contained within.
The store is home to my favourite street ever, 'magazine street', which runs through the store, connecting the separate blocks, and reputedly containing over 30,000 current and back issues of mags and zines from all over. It also houses a Starbucks, Anjin, a fancy low lit dining spot, and a Family Mart. In short, you don't have to leave for a really long time. Warn the loved ones that you're travelling with.
Tokyo retail is big on 'select shops' or shops within shops, which are curated to reflect an overall these. It's an interesting and thoughtful way to shop, and it means that your book-shopping experience can expand to include the purchase of hinoki incense cones and your new favourite tote bag.
The rest of the complex is equally wonderfully put together. You can buy an electric bike, a Leica, fancy pet coats or just sit in the sun and eat fluffy pancakes at Ivy Place.
If you can't make it to Daikanyama, don't despair. All of the Tsutaya shops are a joy. I've spent some happy times perched above the Shibuya crossing eating truffled fries and reading. The Nakameguro shop is another firm favourite, you'll find it adjacent to the Metro station. Whichever one you make your way to, just remember, tax-free shopping.