Deniz' apartment was great for us, it was surprisingly spacious, the location is fantastic, in Kadikoy, just 10-15 minutes away from the ferry port, and surrounded by many great cafés, little stores, and a great atmosphere in general.
The more touristic side of Istanbul is easily reachable by ferry, and we had no issues with that at all. In fact, I would recommend staying in Asia over the European side of the city, as it has a more local flair, which is really enjoyable!
Best Regards,
Max