If you prefer to have the local experience, then I would suggest taking the public ferry. Communiting from Asia to European side (or vice versa) is a lot more comfortable and faster when you take the ferry from Kadikoy to Besiktas (or) Eminonu. A lot of locals use the ferry for their daily commute. I definitely suggest having that experience and feeling the local culture particularly during the rush hour.
Other than that, there are really nice yatch tours organized by a variety of companies. They are little bit expensive, however, taking a yatch tour on the Bosphorus, and being dropped at a restaurant on the strait is priceless. That is a very romantic way of experiencing the scenery.
