They're all located in the Shangri La Hotel. Noodle Bar is the cheap and casual option. It's been a couple years since my last visit to Noodle Bar or Daisho, and I haven't been to Shoto, so I can't comment on recent experiences with the food. I wasn't too impressed with the food at Noodle Bar, that's part of the reason I haven't returned. I was at Daisho for a special group dinner, which was fun, but I don't remember the food being special.
Milk Bar and Nikai ate also part of the Momofuku establishments at the Shangri-la.
Shoto is the fine dining option.
For a quick meal while dining solo, go toNoodle Bar. For a fine dining experience, go to Shoto.
http://momofuku.com/toronto/shoto/ The 10 course set menu at Shoto ($150). Also consider Toronto's favourite splurge, Splendido, which currently only serves a tasting menu, priced at $180 http://splendido.ca/menus/, Alo ($89 for 5 course set menu http://alorestaurant.com/ ) and Yunaghi's tasting menu (which is a relative steal at $80.)