Firstly, as i said before, if there is an uncertainty whether they will accept you in the Phd programming then simple go for Ottawa. There is no need for you to take any risk. Ask the professor and make things clear first if you want to have Waterloo as an option.
No matter how much i want to believe your point of view since many of my friends went to MIT and Harvard, but it is somewhat wrong. A good University will get you to the interview room but after that it will up to your skills. No doubt if you work hard there wont be any disadvantage to you over someone who has been studying at Waterloo or UofT but in the initial stages, it would be easy for you as the name of the University will speak for you. But then again, if you got accepted for the field you want to work in at UOttawa and that is uncertain at UWaterloo then i would advise you not to take the risk. I am just a bit confused because you can do your Phd at some other top US University after you do your MEng and we all know the US Universities have more endowment and you would definitely have more opportunities there as compared to both Waterloo or UOttawa unless of course the Phd program offered by UOttawa isn't offered at any other University.
I would again disagree. The Macleans ranking are specifically for Canadian Universities. All the other ones are not reliable for Canadian schools. Look at the Top University rankings or the Times higher education ranking in Computer Science Undergraduate. While everyone knows in Canada that Waterloo is at the top for Computer Science at the Undergrad level mainly because of the academic and Coop program (UofT is better for grad school), these other websites will show UofT to be higher and even show UBC to be higher which is clearly wrong. Furthermore, Macleans shows the grad school components as well like the research output, publications, citations etc which can give you an idea about it's grad school reputation which is clearly better. At the end of the day, you should choose the University where you'll be happy. If you are happy that you'll get a Phd position at UOttawa then by all means it is the better choice. If i were you, i would have accepted the UWaterloo offer and apply for Phd at a good US school but that would be again my choice and it would vary for you.