Correct me if I'm wrong but rankings are based a lot on the research of the university.
I've heard of many McGill Engineering undergrads who openly say there was nothing special about the program.
They do have some interesting Engineering programs though, no idea if they are any good.
This is true, LL. It really depends on your perspective. Waterloo is a great school for undergrad program. No argument there. Two of my good friends went there and they are happy with their education. I would say that at the undergrad level, Waterloo trumps McGill to a certain extent , especially if they still have a coop program (McGill has an Honours program though, which sets the table beautifully for grad school). However, McGill has great graduate school, and from my standpoint as a BME, McGill, like U of T and UBC, as well as Western, benefit from their proximity to a top medical school. Make no mistake, biomedical engineering is the fastest-rising area of engineering, due to age demographics as well as the appeal of BME to female students, which doubles the talent pool compared to traditional engineering departments.
When I go to international conferences related to BME, I see a lot of papers from McGill, UBC, Western and to some extent U of T (and nearby hospitals); I hardly ever see papers from Waterloo. This take may reflect my BME bias, but fast-forward 10-15 years, and I believe that this explosive growth will continue, BME will rival Mech Eng and Elec Eng in size and scope, at the least. The result will be that Waterloo sees itself handicapped as an engineering school from their relatively small footprint in this area, partly the result of Kitchener-Waterloo (McMaster) not being in the same league in terms of their medical program as McGill, U of T, UBC and Western and not being so close physically as one integrated campus. There would be a way around that, but Waterloo and McMaster would have to be much more proactive about working together. However, for the most part the grunts there don't speak clinicalese very well, and the docs there don't relate to engineers well enough to make the most of that technical brainpower, in the manner that Western is doing just down the pike.
Edit: on a related note, those of you who are doing engineering, I enthusiastically recommend grad school (Master's or PhD, no matter), if you want to really enjoy your career as well as set yourselves apart (provided that you choose well, based on your real interests). As a bonus, those of you doing BME (which is often a graduate program) will actually have a fairly large number of women in your class.