As mentioned, Sydney's is re-opening (this weekend I think actually) - it just had fire damage, didn't burn down. They had the only chain-stitch machine in the city from what I understood.
Nomad is one of my favourite stores here - APC, Engineered Garments, NDG, Wings + Horns, Gitman, etc.
Jonathan + Olivia is solid - just north of Queen on Ossington...a little removed from the other shops. Carry EG, Our Legacy, APC, etc.
TNT Blu has nice stuff but is EXPENSIVE. It's one thing to say Toronto is way more than stores in the US, but TNT had Gitman shirts for $255 when they were selling for $170-90 elsewhere in the city.
Klaxon Howl is a great shop - selection can be hit or miss, but you won't be disappointed you went. They actually did a collab with The Bay last year.
Uncle Otis - again seems to be hit or miss for me, but things seem to getting more consistent.
Get Outside is a solid option for shoes - Red Wings, Sperry, Clarks, Sebago, Quoddy, etc.