It's a totally luck.. Have done this cruise 4 times and the only time the leaves had really changed in all the ports was last time when we went about Oct. 15. It had been warm and then very cold at night (in fact they had record low temps that week in Maine with daytime highs in low 40s and windy). In mid- late Sept. once it was in the 70s and 80s; another time in October they had changed in New Brunswick and outside Halifax in Mahone Bay but not in Maine and another time just a little bit higher elevations in Arcadia. Just book the cruise in mid-October and keep your fingers crossed would be my advice. If they have chilly early fall in Canada the peak may be over but have never really seen in Maine and New England before October.
It's a lovely itinerary IMHO and one that a lot of people overlook. Ports are great, food delicious. If you do a one-way to Quebec City (or from Quebec) leaf peak may be earlier than mid-October as it's further north. That would be my ideal as Quebec is charming city and you get most of the same ports