The Thousand Islands/I-81 crossing is notorious. It is very busy with travelers from the US, many who come to Canada thinking its the 51st state and can just waltz in. The attitude of Canadian customs and Border Patrol there is as bad as the Niagara Falls crossing.
Not sure where you were heading, but get off I-81 take Rt 12 and Rt 37 instead, and cross at Ogdensburg, which is 60 miles of really nice riding with great sightlines and scenery, particularly on the Rt 12 portion. If going to Ottawa or Montreal, this crossing adds nothing to your trip but nice riding and a much smoother ... and significantly faster ... border crossing.