My preference is IST since it is closer to the city, as johnny3 mentioned, and you can get there with subway and tram. But you could potentially find a better air deals at SAW. The question is how much saving you need to switch to a more inconvenient airport (inconvenient here is referring to 2.5 hours to get to SAW; transport there is quite easy during day time--ferry then bus right off the dock).
For me, the price difference was over $150: $260 from IST to MUC vs $100 from SAW to MUC. So I chose SAW to save money.
Budget airlines Sunexpress and Pegasus Airlines fly b/w SAW and MUC. I think Pegasus also has flight b/w IST and MUC.