I just pulled the NY E-Z Pass discount form and looked at the on-line toll schedules. Without spending way more time then I want, yes, there is a discount. What percentage/dollars will take a while to figure out - but it is NOT inexpensive to cross NY State via the Thruway.
There are a couple alternates if you have the time. US 20 is a pleasant drive and pretty scenic. NY 5/5S is also pleasant but a somewhat more challenging drive. I've done them both but with smaller 5ers and TTs with no problem but time spent. There is also I86 to I88. We have traveled I88 and it is usually a work in progress along with way too many deer to mess up your vehicle as I have 2X
Dave W along with my DW, Susan and our poodlepups, Callie & Molly,2011
Ford F250 6.7 CCLB, 5er Hitch Option w/B&W Hitch,,Ride Rite air bags, 2014
Montana High Country 343RL (38')w/disc brakes