The first trip I took that across the channel to the Islands, and it's still a go-to route. You can head through its little river (on the side facing the city) or around the back. Today I took a trip around back, through the Airport Channel, across the front of the city and back to Cherry Beach. I'll share the route and some pictures from the trip.
One important note: at either end of the airport, there are areas you cannot enter with your boat. They're underneath the flight path, so it's probably a reasonable rule, but if you don't know they're there you can easily float into the area. The fine is huge. Little diagram below:
It can be hard to see where these buoys ARE on the West side of the airport, if you're travelling clockwise - the direction I was on this trip; I discovered these by paddling right into the middle of them. Nobody caught me, and I still see people take the shortcuts - but ten grand... You can avoid this by pointing your nose at Ontario Place/Molson Amphitheater.
The water will be its choppiest in the channel where the airport ferry runs.
While you're avoiding the forbidden area on the East side of the airport, you'll also have to contend with Water Taxis and Ferries. Don't even try racing a ferry. If you fuck up it'll be an embarrassing death, cuz all the people on it will be watching. When in doubt just sit still and wait.