There are a few pleasure boats in some of the working ports, at least in NS. This club will accomodate transients but I don't think the site shows that: Isle Madame Boat Club
Here are a few more in the east end of NS & PEI: Cape Breton Marinas
There are a ton of nice free anchorages within the Bras D'Or Lakes. If you're looking to be near a bigger town (Halifax, St John's), it'll be harder to find something close enough to enjoy the town without paying for it.