Bus (or other transportation) from Toronto to Waterloo?

Check with the University of Waterloo, they run shuttle buses to and from Pearson Int'l.

http://www.uwaterloo.ca/

Other than that, Greyhound has service, Though you'd have to go Downtown to pick it up. You can do this by TTC.

Waterloo To Pearson Airport Bus

I would recommend the Via rail route then just walk out the 2 blks to King St and get on the bus from the Fairview Mall to the Main Bus terminal and then the 78 to McPhillips or take the U of W bus right to the campus.

Otherwise there are Greyhound buses to the same terminal, I take the Airport Express to the train station and if you go by bus you will have to get off and go to the corner of Bay and Dundas were the Bus terminal in downtown Toronto is, I get off at the Royal York and walk acrossed to the train station on the other side of Front St, and if you know a dhead of time you can make a reservation on Via and save 30-40% off the one day return or one-way fare, check it out, both the bus and train will cost around $35-40.

Coach Canada