When I was in Winnipeg, I used to order from 49th or buy from Cornelia Bean in a pinch. I have been working in Toronto for the last six months and am quite pleased by the options available here. My two favourites are Te Aro (
http://www.te-aro.ca) and Mercury (
http://www.mercuryespresso.com) both on Queen East in Leslieville.
Te Aro will (apparently) ship free on orders over $40. All their beans are roasted in house weekly on MTW. The Kenya is really nice if you can get it. Mercury gets their beans from George Howell Roasters (Terroir) in Massachusetts. You can order directly from the GH site and believe they will ship to Canada. A little expensive but some really great beans. I have no idea how long delivery takes, shipping costs, etc.
Some others I have come across: Lit on College sells Stumptown; Manic on College sells Intelligentsia; Dark Horse on Queen W sells 49th.
I would Te Aro a shot if you order and are looking for something new. It's quite a great place. I wish Winnipeg had something similar.