I have flown with several regional pilots who require special permission to enter canada due to DUI's. They can't enter through the "crew" line, they have to go to the special office for criminals, dissidents, and terrorists. You might want to re-investigate getting a waiver or whatever they call it.
Any airline is going to ask if you have had a DUI...it's not a good thing but it's not always disqualifying at a regional. Since yours was a few years ago (hopefully you were young) they might be willing to entertain the idea that you've matured (you seem to have the right attitude about it).
Also, some regionals don't go to Canada...look at their route maps. Maybe Piedmont or PSA?