Two years ago did a nice trip in the area:
Day 1 Gananoque to Kingston with side trip to Howe Island - 54 km
Day 2 across Wolfe Island to Cape Vincent NY, then to Alexandria Bay - 61 km
Day 3 across 1000 Islands bridge back to Canada, then to Brockville - 63 km
Day 4 cycled a loop north of Brockville - 62 km
Day 5 Brockville to Gananoque - 44 km

Had wanted to do Alex Bay to Brockville via Prescott/Ogdensburg bridge, but bikes are not allowed. Winds can be strong in the 1000 Islands area so be flexible unless you are a masochist.