Not quite Toronto, but me and my buddy make monthly trips to Catacombs in Kitchener. It's about an hour away from T.O.
Since I heard of this place, I entirely bypass Toronto for my merch shopping! You can check out their stuff at their website: http://www.catacombscds.com ,got my WoY beanie from there a while back.
There is a badass CD store a few doors down from them called Encore Records. Tons of new & used metal CDs and some DVD, Vinyls.
Sorry man, I made a mistake or sorts. Sonic Boom didn't use to have t shirts but they do now. A pretty decent selection actually, if you don't mind paying 25$ plus tax.