Back in Fall 2010, I had the pleasure of doing an academic exchange to Istanbul. Here's an album of ferry photos I took while there: imgur.com/a/zBCpz
There are two main companies that service Istanbul: Şehir Hatları (white and buff, more classically-styled) and Turyol (white with green and blue trim, more utilitarian, narrower vessels). These two are responsible for bringing traffic between the European and Asia sides of the city, as well as to/from the Princes Islands nearby. Prices for both are similar, and both are integrated into the overall Istanbul transit system's fare system (tap card, etc.). They also have a snack and drink service on board, with hot tea, coffee, and sahlep available for purchase (both at the 'bar' and via roaming waiter!).
The third company you'll see is IDO, which stands for İstanbul Deniz Otobüsleri, or Istanbul Sea Buses - their blue-and-white catamarans connect cities all along the Sea of Marmara, as well as providing an express rush-hour service along the Bosphorus to take people between downtown and the suburbs to the north. This is most similar to BC Ferries.