I traveled throughout Turkey last summer with a friend who's very well traveled and insisted on a hotel with a view of the Bosphorus. At the time we were booking protests were taking place in Istanbul so the Hilton was taken out of contention.
An old friend, from Turkey, suggested this hotel, Sumahan.
It's on the Asia side of the Bosphorus and sits right on the water. An old brewery that was converted to a small hotel. A husband/wife couple (both architects) redesigned the building and their daughter (an interior designer) decorated.
Best of all, they operate their own launch to get you back and forth across the water.
If I were returning I don't think I'd stay anywhere else!
http://www.sumahan.com/