It turns out that there are two other towns in Ontario that are right up there with Waterloo. Richmond Hill actually comes out slightly on top using the NHS figures (47.3% vs Waterloo's 46.8%), although I suspect that's within the sampling error. Oakville is also in the top group with 46.1% of its population with university degrees. There's then a noticable drop to Ottawa in fourth place (42.8%).
The Waterloo ranking is for the City of Waterloo. The numbers for Waterloo Region aren't as high, with Kitchener ranking 44th and Cambridge 116th in Ontario. London ranks 29th.