You can avoid the NY Thruway and associated tolls by taking I-86 and I-88 rather than I-90. If it's purely a financial question, it's really a tradeoff between the cost of gas vs. the cost of tolls for your rig.
All the northeast state toll systems are part of the EZ-Pass consortium (including the Illinois iPass), and all interoperate. Some states offer better deals for non-residents than others. If you'll be traveling the New York thruway with a motorhome (but not an RV trailer), then signing up for the NY motorhome thruway plan is a good deal; motorhomes pay the equivalent car rates given the number of axles and trailers and so forth. For a two-axle motorhome with nothing in tow, that works out to about half price, or around $15 saved each way on this trip.