New York City (USA) and Montreal (Canada) are connected to the Atlantic Ocean via the St. Lawrence River / Great Lakes system.
While NYC and Montreal are on different rivers (Hudson vs. St. Lawrence), they share access to the Atlantic Ocean and are linked by the Great Lakes–St. Lawrence Seaway (opened 1959). A ship can sail from the Great Lakes to Montreal, out the St. Lawrence to the Atlantic, and down the coast to New York Harbor—all on connected, navigable waters.
Thus, they are the two major North American cities that "share a common waterway to the Atlantic" in the sense of a continuous inland–ocean shipping network.