Best route is still I-90 all the way. Chicago can be tricky, but if you catch it at the right time you can get through it with minimal hassles. Your NY EZ Pass is good all the way through to the coast. Cleveland can be a bit of a challenge with Dead Man's Curve on 90 but other than that I-90 is a pretty good road. I like to call I-90 the Main Street of the North. Great scenery along the way also.
I should add, that it does depend on when you go in October. Early October should be fine going over the passes, late October not so much.