Take the mid-morning Bosphorus Tour ferry from Eminönü and you get to Sariyer on the Northern Bosphorus about 75 minutes later, just in time for a nice seafood lunch at one of the little restaurants north of the Sariyer ferry dock.
You can catch the ferry south to Istanbul a few hours later, but I prefer to go by land along the shore to visit some of the sights I glimpsed on the ferry voyage north.
Transport
Taking taxis is the quickest and easiest way, but as it is 22 km (13.6 miles) from Sariyer to Eminönü and the Galata Bridge, the fare may be around YTL30 or so.
Bus 25E (Sariyer-Kabatas) goes south along the western (European) Bosphorus shore to the ferry docks, tram terminus and funicular at Kabatas, the scenic route taking about two hours (127 minutes, average) for the entire run. Buses depart Sariyer about every 15 to 30 minutes depending on time of day. (Schedule)
Bus 25T (Sariyer-Taksim) goes along the Bosphorus shore as far as Büyükdere (for the Sadberk Hanim Museum), but then turns inland and travels through the hills to Taksim Square (125 minutes, average). This is the less scenic, more 'city' way to go, and you can't stop to see the sights on the shore. Buses depart Sariyer about every 15 to 30 minutes, depending on time of day. (Schedule)
Bus 30D (Yenikapi-Ortaköy) connects the fast ferry dock and suburban train station at Yenikapi with Eminönü, Karaköy, Kabatas, Besiktas and Ortaköy. It does not go north of Ortaköy, however.
Minibuses depart periodically, going shorter or longer distances; many of them go up into the hills rather than along the shore. Mention your destination to the driver before boarding to be sure you'll get where you want to go. Sariyer-Taksim minibuses go all the way to Taksim Square, and faster than the bus, but usually on an inland route.
What to See
Here's the order of sights from north to south. If you're heading in the opposite direction (south to north), just read upwards from the bottom! The distances by each name are from Galata Bridge on the Golden Horn.
Sariyer (22 km, 13.6 mi)
The town near the northern mouth of the Bosphorus is good for a seafood lunch before heading south along the shore. More...
Büyükdere (19 km, 12 mi)
Just south of Sariyer, stop here for the fine Sadberk Hanim Museum. More...
Tarabya (17 km, 10.6 mi)
Called Therapia by the Byzantines, this pretty cove has been a healthful summer resort of Istanbul's elite for centuries. More...
Yeniköy (13.5 km, 8.4 mi)
An elite summer settlement since Byzantine times (when it was named Neapolis, "New Town"), it still boasts several grand old "summer embassies."
Istinye (13 km, 8 mi)
This well-protected bay was a shipyard in both Byzantine and Ottoman times. A road leads inland to the district of Levent, in which you can board the Metro to Taksim Square.
Emirgan (12.5 km, 7.8 mi)
Noted for its April Tulip Festival, Emirgan's gardens are a pleasant place to take a rest and have some tea, coffee or a light meal.
Fatih Bridge
The Fatih Köprüsü (Conqueror's Bridge), beautifully visible from Rumeli Hisari (and vice-versa) is named for Mehmet the Conqueror.
Rumeli Hisari (10.5 km, 6.5 mi)
The mighty Fortress of Europe was built in just four months during 1452 on orders of Mehmet the Conqueror. Commanding the narrowest part of the Bosphorus (about 700 meters), it cut off Byzantine Constantinople from its grain supplies from the Black Sea coast, making it easier for the sultan to conquer the city in 1453. More...
Bebek
The town of Bebek, with its pretty bay, is on Rumeli Hisari's south side. Bosphorus University, founded as Robert College by New Englander Cyrus Hamlin in 1863, shares the hillside with the fortress.
Here's a full-day itinerary for exploring the Bosphorus in Istanbul: cruise on a traditional ferry from Eminönü near the Galata Bridge up the Southern Bosphorus to the Northern Bosphorus, get off the boat and have lunch in Sariyer, then travel south by land along the European shore, stopping at the major sights which you glimpsed as you cruised north. (For a shorter 1.5-hour cruise, go by TurYol boat.)
Eminönü: Bogaz Hatti Ferry Dock (No. 3) (10:00 am)
Although the ferry doesn't depart until about 10:35 am, get to the dock early to buy your ticket and get a good seat on the boat. The port (left) side will be sunny, the starboard (right) in more shadow; outside seats are cooler, inside seats warmer.
Bosphorus Cruise (10:35 - 11:45 am)
Sariyer (11:45 am - 13:30/1:30 pm)
Stroll around busy Sariyer, enjoy the ambience and choose a place for lunch, preferably one of the seafood restaurants on the Bosphorus shore.
Sadberk Hanim Museum (13:45 - 15:00/1:45 - 3 pm)
Spend an hour or so in this marvelous art and antiquities museum.
Rumeli Hisari Fortress (15:45 - 16:45/3:45 - 4:45 pm)
Climb the castle walls for the marvelous views.
Ortaköy (17:00 - 18:00/5 - 6 pm)
Stop here for a rest, a drink hot or cold, a snack or meal, and some pleasant people-watching.
Eminönü (19:00/7 pm)
Return to Eminönü in time to clean up and go out to dinner.