Cheapest way is taking the 192 Rocket (bus) from the airport to Kipling station (can't miss it) which is $3.25. From Kipling you can get downtown - same ticket takes you onto the subway.
Kipling to Yonge is 30-35 mins, down to Union is about 10 mins normally. The Union express bus is faster I believe, though last I knew it was about $30.
CN Tower and Ripleys are both extremely overpriced and not that great in my opinion (note; I've done the CN tower twice day and night and was disappointed both times, I've not done Ripleys but have only heard negative reviews). The zoo is meant to be very good but is a heck of a trek on public transport.
Depending upon exactly when you land the High Park blossoms are meant to be out early this year and a of people like that. It's also quite a decent park (400 acres) generally. There's a little zoo (not amazing though) in the bottom areas. That's either Kipling->High Park TTC @ 15 minutes (plus bus to Kipling, 20-45 mins depending upon time/traffic) or Union->Yonge->High Park (30 mins). Or it's $45 by taxi from Pearson, that's standard rate without tip.
But personally, if it were me ... I'd hire a car and drive to Niagara. It's only about 1.5h from the airport. It's far too commercial for my liking now, but still worth a visit. Again at this time of year I'm not sure which attractions - maid of the mist etc... - are running. You can bus it to Niagara but you'd need to head downtown first and especially at this time of year I wouldn't want to risk the connections.
What are you planning on doing with your checked luggage for these 12 hours? Most airlines have a 4h checkin limit (Air Canada does). For me that's +1 on the car option