I've researched this considerably, and really don't think any exist. There is Peter Alexander (the Gunsmith of Grenville County), a well known and respected maker of flintlock rifles who is currently active, but I don't think he makes any percussion guns. There is also John Clark (Clark Industries) but he doesn't seem to be building guns anymore. I've heard a couple other Canadian names mentioned here and there but I really don't think there are any active gun makers in Canada, specializing in traditional black powder guns.
Flintlock long guns are not considered firearms and can be bought/shipped back and forth over the US border without restriction (other than international shipping costs), but not so for percussion guns and you'd have to use an importing service.
Within Canada, probably your best bet for a percussion rifle is to find one used or buy a new T/C GPR or maybe a Pedersoli.