We stayed at the Seven Hills hotel just a block or so from the Haigia Sophia. The restaurant is on the roof and you get great views. Food is very good, especially seafood. They have local wines on list. Really enjoyed a 2010 DLC Kalecik Karasi (Doluca).
The Cihangir neighborhood not too far from Taksim has a lot of great little restaurants. Van Kahvalti Evi has a nice Turkish breakfast. Around the corner, Datli Maya sources some of the best regional products from around Turkey for a not-so-traditional take on modern Turkish. The best kebab I tried is in the Pangalti Kurtulus neighborhood at a place called Adana Ocakbasi.
In general, Istanbul Eats is a good resource and I love the Eating Asia blog posts about Turkey. They are food bloggers based in Penang Malaysia that have visited Turkey a few times with some great write-ups.
Unfortunately, we never made it to Ciya, as hoped. We did, however, find a fantastic kebab place called Ali Ocakbasi. It is in a hard to find little side street called Grifin Han in the Karakoy neighborhood. The wine list was modest, but good. The food was simply superb! And the place is right on the water with unobstructed views. Very attentive service. Probably our favorite find so far.
Check out this article from the Washington Post about a fabulous sounding eating tour of Istanbul:
Istanbul Eats
Offers two tours, one in the Old City and the other in the more cosmopolitan Beyoglu, for a maximum of six people. The cost is $125 per person and includes “as much or as little food as you want,” says originator Ansel Mullins. “All we ask is that you try a bite. That’s our thing.”