I was also accepted to both UofT's MPP and Queen's MPA programs (as well as two other schools). I have to admit that Toronto was my first choice, though conveniently, their program also offered me more in funding than Queen's did.
To me, when I did my research, UofT had a more complete program, better course offerings, better instructors, far superior internship opportunities (and a mandatory paid internship at that - great experience, plus Queen's does not guarantee an internship), and above all, better networking opportunities. There is also a certain amount of prestige attached to UofT's program. I have siblings who have previously attended/are currently attending graduate programs at UofT, all of whom found great benefit in the university, and (those who are finished) have found that being a UofT grad really made a difference to potential employers.
Major upsides I considered with Queen's MPA: shorter program, lower overall cost.
Ultimately though, I decided that, in the long run, the extra time and cost of going to UofT will be more than worth it.
Best of luck deciding !!