My suggestion: instead of going over the Thousand Islands bridge, ride to Cape Vincent, take the ferry over to Wolfe Island (it's $5 for bikers), ride across Wolfe Island, then take the free ferry into Kingston. It's a beautiful ride, you avoid the very very narrow walkways on the bridges; you avoid the long lines at the border (the ferry to Wolfe Island holds maybe 10 cars at the most, so the border crossing goes quickly) and while you wait, instead of being stuck in long lines of cars, you are right at the river's edge; and you save yourself something like 40 miles:

Black River NY to Kingston ON via ferries

Here's a link to Info on the ferry from Cape Vincent to Wolfe Island

ANd the ferry from Wolfe Island to Kingston


Looks like a great trip!