When in Nişantaşı, there are two places I visit almost every time: Kantin (check the Kantin article) and Patika Kitabevi. This charming bookstore deserves your time with its variety of books and magazines so it would be wise to go there when you are not in a hurry.
Patika is the one if I am looking for limited editions, rare or out of print books. They also sell several international magazines which are not very easy to find in Istanbul. Coffee table books on Turkish art, history and architecture decorate the window display. At Patika, you can also find classics and bestsellers as well as fashion, design, photography and travel books in English and Turkish.
The big communal table is great for browsing through books and magazines while having tea, coffee or dessert from the mini café inside. Patika has a friendly staff who are eager to help and inform if you are looking for something specific. I think it is the best bookstore in Nişantaşı along with Pandora which has opened a new branch on Valikonağı Caddesi.