I think this question would be better posed about 10-15 years down the road. Apart from The National, the best courses in Canada since 1949 have been built in the past few years, or will be built in the next few years.
Banff, Jasper, St. George's, Capilano, Highlands, are in rarified air...great sites, great design.
Courses (post 1949) that I've played which may possibly approach Thompson's best include...
Eagle's Nest
Devil's Paintbrush
The National
Redtail
Osprey Heathland and Hoot
Cottage country courses such as Bigwin, Grandview, Rocky Crest, Lake Joe, Wildfire, Taboo, etc. are excellent and unique in their landscape. I know there are more up there, too.
It does seem the US has been more successful in getting more GREAT courses built in the last 50 years. We can't deny the obvious fact that a main reason for this is the architects that have been working in each country. Would have loved to have seen Doak, C&C, etc. get a few of the recent projects up here on very good sites...just for comparison sake.