When we were booking our NYC - Quebec City, our TA said to start in NYC (we are taking a car service to the port) and flying home from Montreal. She said with the state of the airlines, canceling flights and delays in luggage, it will not matter on the trip home. Worst case, we can spend and extra day in Canada or if our luggage does not make our flight, they can just deliver it to our home.
Sounds like it was the right choice to make.