I'm assuming you'll be paying OOS tuition at Geisinger (~$64k) compared to IS tuition at SUNY (~$44?). This alone should seal the deal and makes this a no-brainer for SUNY Upstate.
I could see the 2 years preclinical giving you ample time to conduct more research compared to a condensed curriculum though so it's not the end of the world. Paying an extra ~$20k/year for 1.5+2.5 vs 2+2 is not worth it.