Before it closed last year (I think), Elk Island was the best nine hole golf course I'd been to. Nine holes from Stanley Thompson about an hour east of Edmonton, with some of the most aggressive fairway contour anywhere---in parts, it makes Highlands Links' famous fairway movement look small!
The 7th, below, was one of the best drive-and-pitch holes around, with a Hog's Back fairway pushing balls from the middle. Anything left was blind and had to play over a severe false front-collection area short left, and anything right went over a mound that was just over 100 feet higher than where you're playing from.
I'd take Elk Island over Hooper, as an example of its quality, but it's close (and I haven't been back to see the recent work so I suspect that's probably changed).
I'd contest that Norfolk in southern Ontario and Kenogamisis (another Thompson) in Northern Ontario should be here -- Musselburgh is a cool golf course and experience, and Winter Park is a fantastic set of greens without much interest off the tee, but I'd take Norfolk and Kenogamisis over both. I'd likely have Kenogamisis over Northwood (30), and then Norfolk behind Northwood
Likewise, Toronto Hunt is a very charming nine hole golf course and a blast to play, but I'm not sure it's top 5 in Canada, let alone deserving of being the only one on the list. That said, it's better than Musselburgh.
Lots I need to see and explore on this list though!