I just got back from Istanbul and am now settling back into life in Chicago. During my time there, I got help from this site called Istanbul Eats. You guys should really check it out to plan the eating part of your trip.
If you're ship comes in at Karakoy there is a nice place nearby called Karakoy Lokantasi. Though there is no view it is a fine restaurant with a wide range of local meze.
Micla at the top of the Marmara Pera hotel is a fine dining experience, a bit fancy in my opinion. NuTeras is a hip place for a view and decent food.
my all time favorite for a view and GREAT food is Abracadabra in Arnavutkoy.
Melengec is also interesting Aegean cuisine- you'll never see so many different greens.