You can transit Canadian waters and yet not "enter" Canada. To make it simple, unless you clear Canadian Customs, you have rights to what is known as "Innocent Passage". The locks at Sault Saint Marie are an example of a place where passing ships do not have to declare entry... even though one of the locks is in Canada and the other is in the USA.
A bit of a segue, but the bottom line is that I am more worried about being boarded in New York Harbor than anywhere in Canada.
The St. Lawrence Seaway, opened for navigation by large ships in 1959, is an example of a legal and an administrative regime wholly devised and controlled by the two states (the United States and Canada) that share it. Based on a river in part, the seaway was developed with the construction of bypass canals, locks, and channel improvements, sometimes wholly within the territory of one state. In 1909, Canada and the United States consolidated and extended a number of earlier piecemeal arrangements in the Boundary Waters Treaty (36 Stat. 2448, 12 Bevans 359), to give both nations equal liberty of navigation in the St. Lawrence River, the Great Lakes, and the canals and waterways connecting the lakes. An international boundary line was drawn generally along the median line of the lakes (with some variation in Lake Michigan), but both nations were to exercise concurrent admiralty and criminal jurisdiction over the whole of the lakes and their connecting waterways. The admiralty jurisdiction reflected a disposition to treat the lakes as the high seas. This view was supported by the U.S. Supreme Court in United States v. Rodgers, 150 U.S. 249, 14 S. Ct. 109, 37 L. Ed. 1071 (1893), when it referred to the "high seas of the lakes."