From PA E-ZPass FAQ
I sometimes pull a camper or trailer with my vehicle.
Can I still use my transponder? Yes. On the Pennsylvania Turnpike, if the weight of the camper or trailer pushes you into a higher class of vehicle, the higher toll will be charged to your account. If you are traveling on other E-ZPass agency toll roads or bridges, please contact the appropriate agency for further information. Refer to the list participating agencies on FAQ # 2.
I would think NY E-ZPass would be the same but as the above says you may want to check with them.