Welcome to cruise-chat. As you undoubtedly know by now, there are a number of possible itineraries for the Canada/New England (C/NE) run. I've done about a half dozen of these cruises, and would highly recommend an itinerary that includes a port stop in Quebec City. It's an amazing city and also offers a contrast to the other ports of call typically on a C/NE cruise (which are wonderful, as well). It is also very exciting to sail down the St. Lawrence River...and what a view that would be from your balcony.
Just a few words on fall foliage from someone who lives on the New England coast -- its timing is unpredictable, and the best foliage is further inland. So, while this is certainly a criterion to use when selecting time of year, be sure to select an itinerary that has a variety of ports of call that interest you on their own.