I take the Beşiktaş-Üsküdar ferry every day, twice a day, to and from work. It is absolutely glorious, especially in the evening, around sunset. I am so happy about my commute I may never leave the city again.
That said, there are actually two companies that offer this service: Sehir Hatlari is the public one, it's run by IETT. The ferry I take is great because it's largely empty, even during rush hours -- its a new route so people prefer the tried and true competitor, Dentur Avrasya. So why do I choose Sehir Hatlari? Well the truth is, it depends on the timing. Unlike the other ferries, it runs on a schedule, so I know exactly whether or not I need to run to catch it. If I run toward the other ferry, it leaves at random times, and I'm usually seconds late, and arrive only to see it slowly pulling away from the pier. Not so with Sehir Hatlari. I know well before I begin running whether or not I can catch the ferry.
I like to stand on the back, on the bottom level, near the bathrooms, because no one else stands there and when I wave at the tankers entering the Bosphorus to welcome them to Istanbul, I can do so in complete privacy without feeling embarrassed.
The negative points are that this ferry, while faster en route, approaches the dock SO EXCRUCIATINGLY SLOW. It's painful. I hate it. It's also always too hot during the winter, and freezingly a/c'd in the winter. Another problem is that people always smoke cigarettes on the back (where I like to stand), even though there is a 69TL fine. No one enforces it and I get angry. The most trivial issue with this ferry is the fact that the water splashes you if you stand to close to the rail.
In general, if I were to recommend a specific route along the Sehir Hatlari, choose the Uskudar-Eminonu one. You'll see the best parts of Istanbul, and it's a 20-minute ride. read more