My personal favorites are Pandora and Robinson Cruise in Beyoglu and Kabalci in Besiktas. For more scholarly books, Homer Kitabevi and Zero Books in Beyoglu. In all those you can find books in English.
If you are intersted in old books visiting "sahaf"s (second hand bookstores) may be rewarding. Eventhough majority of their collections are in Turkish they carry books in various other languages. Some of the most well knowns are in Beyoglu and Kadikoy. Simurg in Beyoglu is a favorite among many Turkish journalists and writers. I am from the Asian side, the ones on the Asian side are more appealing to me perhaps due to their familiarity. There are quiet a few you may come across if you walk from Kadikoy Carsisi to Moda Burnu. My favorite is Dagarcik Sahaf in Moda.