Been awhile since I have been up there, but I 2nd St. John's and the river. It is quite incredible to transit the reversing falls on slack tide then go back by car and see how violent they are when the tide is moveing, Beautiful cruise up the river.
Halifax is another great stop, not a bad place to lay over if you need to wait for guests, tie up at the Maritime Museum.
I have not done them, but the Bras D'or lakes are supposed to be great cruising, as well as the Canso canal area and on up to PEI.
More than likely going to need a pilot for a lot of the Canadian waters as well, glad to see you are doing something different.
Oh yeah, check out Lunenburgh as well I think.