I found that Google maps doesn't provide public transit functionality in Istanbul, so I'm curious what apps natives use?
This recent post from The Istanbul Guide website mentions a few general-purpose apps including:
Trafi Türkiye (Free, English and Turkish, iOS and Android)
Working with real time data and timetables, this app pretty much unlocks the wondrous world of Istanbul's public transport. This well designed and easy to use public transport map gets you from A to B using ferry, tram, metro, and bus. Whether you enter an address or just drop a pin, Trafi will suggest the nearest available route including transfer points and approximate duration. Check customizable Twitter feeds for news, or look at schedules and transport network maps. The app currently provides data for Istanbul, Ankara, İzmir, and Bursa
Google Maps supports public transport since one year in İstanbul and you can use Citymapper app for detailed options. Citymapper is providing better results and have better interface from Trafi.
Not better than Trafi Türkiye, but Yandex works well in Turkey with detailed directions. (At least better than Google Maps)
Additionally IBB Trafik provides up-to-date traffic information. So you can learn where there is an accident, construction or traffic jam. I think it will be useful while planning to travel because Istanbul is also famous with its traffic jams and if you do not check the updates it might take more than 2 hours to travel somewhere within Istanbul.