There are so many!
Bebek Kahvesi is definitely one of them. Bebek is up north, close to the second bridge (Fatih Sultan Mehmet bridge). This is a cute little bay where many private yachts are docked and you can just sit by the water, have your tea and watch the cargo ships, ferries and private yachts go by.
House Cafe in Ortakoy is another great location, where you can either have your tea or their delicious homemade mint lemonade and watch the ships go by.
Kabatas also has a nice and very casual tea place where you sit on plastic chairs and watch many ferries go back and forth (since Kabatas is also a very busy pier).
Another great option is to visit Moda on the Asian side and sip your tea at Moda Çay Bahçesi. Here you can watch the sun go down behind the Prince Islands and feel as if you are in a small beach resort as opposed to one of the biggest cities on earth.