I consider myself as someone who knows my bagels and have two favs in the city to share.
Hands down #1 - a new comer Bagels on Fire on queen street in the beaches. If you go in around 7 or 8 in the AM you can usually get some still warm from the wood burning oven.
I used to enjoy st urbain and grabbed one (and it was still warm) as I ran through SLM and was really let down. I've grown accustomed to the top notch quality of bagels on fire and was let down.
Second place for me is nu bagel in Kensington market. A very close second but a tad 'uppity' in attitude and expensive from what I recall if buying by the dozen. Also they open late - I was driving by early one Sunday am around 9, and they still weren't open for the day.
If you love bagels or happen to be passing through the beach, give bagels on fire a try - you won't be disappointed!