Canada and New England cruises sail mostly in September and October, for the fall colors. Those same weeks bring the first nor'easters of the season: coastal storms with cold rain, strong wind, and rough seas that can last two or three days. Hurricanes that start in the Caribbean sometimes track up the coast too. By the time they reach Nova Scotia or Maine they are usually weaker, but they still bring heavy rain and wind.
Temperatures change fast this far north. A cruise can leave Boston in shirt-sleeve weather and reach Quebec City or Newfoundland a few days later to cold wind off the water and coat weather. The average for a date hides that swing, so a long-range outlook can look warmer and calmer than the trip turns out.
Cruise lines skip or swap a port when a storm makes the harbor unsafe, and tender ports such as Bar Harbor are the first to be skipped in high wind. Pack a warm layer, a windproof and waterproof jacket, long pants, and closed shoes whatever the forecast says. Travel insurance that covers missed ports and weather delays is worth a look for these sailings.