Istanbul: suggestions for tour guides and other activities?

The best thing we did last May was to book with Istanbul Eats on our first full day. We took the old town eating tour from around 9AM-around 2PM. We sampled the food, drink, and CANDY in the back streets of the old city where the Turks live, work and eat. The tour was a bit pricey but well worth every penny since that gave us the confidence to return again and again to places off the beaten path to shop, explore, and eat. The prices are much cheaper at the mom and pop places where the locals eat and prices are posted on the menu boards. The Turks are extremely fastidious about cleanliness so there is no worry about eating anything exotic. I loved all of it, even the lamb pancreas sandwich and the fermented millet drink. Yum! We met up with our guide right outside the spice market and off we went. We spent five full days there and never got across the Galata Bridge to the modern Istanbul side. We did do the full day tour on the Bosphorus to Anadolu Kavagi and view the opening to the Black Sea. We also spent one day on the Asian side of Istanbul, shopping and eating of course. We also did the touristy things, most of which are close together and easily walkable. No tour guides needed for the famous mosques and museums or the Topkapi Palace.
The Turkish people from all walks of life are extremely courteous and helpful. Our hotel staff in the old town (Sultanhamet) were also very helpful with recommendations about what to see and where to eat dinner with a view of the Golden Horn. If I were you I'd leave Bourdain's suggestions behind and let the hotel staff help you with that. You will be smitten by Istanbul, which has become our all-time favorite city, replacing Paris on our list of must-return cities.

I think the best combination for what you are after is to visit several very close neighboring towns at the coast of Bosphorous on the Anatolian side. You can take a boat to those places and you will find good restaurants, nice views and some still remaining local touch. I would start the boat either from Eminonu or Besiktas(Check with your hotel though) and get off at Cengelkoy or Beylerbeyi. Have a good trip.

Andrea, I am so envious- As George has said, Istanbul is my favourite city in the world too. George I love the sound of what you did, and next time I'm there, I think I'll do the same.
One of the things I did was to get up really early and walk around the old city. It has quite a different feel then (it's a thing I like to do in most cities).