I live and sail in Nova Scotia (LaHave River Yacht Club), but have not sailed to the Bras D'Or Lakes or to PEI yet. I know both from a land lubbers point of view and have only ventured down to Liverpool and up to Lower Ship Harbour. This summer we plan to do Cape Breton. The best and most up to date guide book I have found is Peter Loveridge's
http://cruisingguidetons.blogspot.ca/but that being said there are lots of spots that are not marked real well in some of the harbours when you work your way up our coast.
Richard