I went up to that area in August and September 2015, and my blog has photos of some of those places, so check it out here:
http://grandmajjb.blogspot.com/2015/08/ A warning about Prince Edward Island--most places there close after Labor Day, but the main
Anne of Green Gables sites were open. Also, remember that the weather can get chilly there in fall.
A BIG WARNING is that fall is a big tourist season in that area because of changing leaf colors. Also, in places along the New England and Nova Scotia Coast, Fall is also when the big cruise ships stop by for the day. For example, Bar Harbor is wonderful, but can get cramped when two big cruise ships are parked in the harbor and disgorge thousands of passengers! Lunenburg and Peggy's Cove in Nova Scotia are not to be missed, but they are small towns that can be packed when a couple of big ships arrive and bus people over to these areas in Nova Scotia!! Ship schedules are planned long in advance, however, and you can check them out to determine when is the best time to make reservations!!!