That's a claim which, from looking at a map, is unlikely to hold up; internal waters are lakes, rivers, and inlets which come further in than the baseline established by the coast.

The only exception I can find is for nations which are made up of an archipelago of islands, and Canada is not one. So again, so long as there's a wide enough route through the islands, it doesn't matter what country owns the islands -- the sea passage between them would be open to international shipping.