Honestly, as an Easterner who went to the Midwest for medical school, I can say that both UW and UI are better schools that Upstate. (I'm at UI but I did undergrad in NY state and originally had no clue about midwest schools). This obviously isn't a universal truth, but the folks I know at Upstate are not happy. You might stand a better chance of matching at mid-tier NY programs just based on the ease to do away rotations and any "geographic" advantage (some residency programs are interested if you have ties to the area, as this may mean that you'd be more likely to rank their program higher in the match). I doubt Upstate would have much influence on CA programs.
The folks I know at UW enjoy both the school and the city. I've heard that their clinical training is good in most if not all depts. I've seen their match list and it's fine. It's certainly known in the Midwest as well as the coasts.
I'm at UI, and I didn't appreciate our school and our rep until I got here. I don't think we get a lot of attention in some circles, but we always have a fine match list and people have no problem getting NY or CA residencies. A lot of people in the academic medicine community see Iowa as a strong or up-and-coming school. I'm not sure how they worked it, too - but I know several OOS-ers who took 1 year off (either before school, or as a fellowship between m1/m2 or m2/m3) to gain residency status for tuition purposes.