There's a whole thread dedicated to
IC Toronto Centre vs IC Toronto Yorkville.
I've stayed at both InterContinentals and liked them both. Kinda depends on what you're planning to do in Toronto. My niece liked the kids check-in counter at IC Toronto Centre, it's close to the CN Tower, and I seem to get better upgrades there. IC Toronto Yorkville is right by the Royal Ontario Museum and shopping. It feels a bit fancier to me.
Split your nights and stay at both!