If you train at Toronto City Centre then Island Air is the hands-down winner. Bigger fleet, lots of good instructors, they can take you to multi/IFR. ATI is a smaller operation and has been rumoured to have money problems for some time now (they've got two Katanas that have been sitting on the apron more than a year with no props). The downside of training at YTZ is money- you'll pay about $10-15/hr more, plus a few bucks for the 30-second boat ride to the terminal (it's on an island). The upside is that it's located right in the heart of the worlds best city in which to live
Oshawa is also a good place to train (it's five minutes from the practice area) and the Brampton Flying Club is a first-class facility. If you're going for a PPL I would recommend YTZ or Oshawa- both these airports are towered and I've noticed that pilots who train at non-towered airports are not comfortable talking to ATC and flight-plan away from control zones, unnecessarily limiting their options.
Best time of year to fly here is May-June and September-November. Winters here can be brutal and the summers tend to be hazy and bumpy.