Wow, I had no idea U of T offered such a tiny bonus to incoming SSHRC holders! I always thought they had mad money. (Some schools offer 10K for the first year if you come in with an external award.) Have you spoken with the graduate program director at York about discretionary funding? My suggestion would be that in the case (likely, I think) that you are accepted to both schools, you should let each director know that you are considering offers from both schools, and need to base your decision partly on the amount of funding support you are offered - often, there is a discretionary amount of awards (fellowships, assistantships, or whatever form of funding that dept has been allocated for admissions purposes) that a program director can offer to students they'd really like to see in their program, but for whom they have to compete with other schools.
It might sound a bit ridiculous that departments compete for students, but they often do - and you're a SSHRC contender, so it's clear that you are a great student. Often it's just a matter of asking for support - f they have the budget for competitive offers, they are happy to spend it. I worked as a graduate program coordinator for a couple of years at McGill before going back to grad school, and I saw these kinds of requests & approvals all the time during admissions.
All that said, who do you really want to have as your supervisor? Which department seems better for your research and long-term goals? Do you think your supervisor will be able to help you make connections and find you more funding/research opportunities and fieldwork? I think that's probably more important for your whole PhD than a few grand, if it comes down to that.
Good luck with SSHRC!! I just got confirmation that they've received my application, too, so fingers crossed.
