The Tophane district in Istanbul is considered by many to be the birthplace of the Nargile, and there are a TON of cafes there. If you get off at the tophane tram stop, you'll notice a huge cluster of them right by the modern art museum (follow your nose!), all of which are recommended by people who do a lot of smoking.
For me, however, the nargile itself is secondary to the setting. I'd suggest take the tram one stop further to Findikli. Get out and head towards the waterside park. If you walk along the strait about 100 feet, you'll find a little cafe with a boat's wheel as the logo. They have a 2-lira too expensive nargile, terrible service, and one of the best views of the bridge and the water in the city. I think it's worth it.