Don't know your budget, but the Royal Ontario Museum (ROM) and the Ontario Science Centre are always pretty cool, although admittedly I haven't been in years. There's a castle in downtown Toronto called Casa Loma that's interesting if you're into that sort of thing, although 2 might be a bit young.
You can take transit to Wonderland.
https://www.canadaswonderland.com/bl...-to-wonderland
If you're flying to Pearson, there is a train that goes right downtown (not sure where you'll be staying). Alternatively, from out east you can definitely fly Porter right to BIlly Bishop. There's a tunnel from the island to the mainland, but there's also a ferry.