My $.02 is that if you can't go to Yale for a Ph.D. (although you should check out the Religious Studies dept before you say that for sure!) you should go to Yale - only b/c it won't be an option for a Ph.D. Otherwise...well, I think debt and quality of life are great ways to examine which you'd prefer. have you visited each place? Visiting often will make the decision for you. Also, talk to other grad students that are there.
Nothing guarantees admittance into a Ph.D. program, even if you're "perfect," as so many people on this board will tell you!
I ended up at Harvard for my MTS, although I had also been admitted to Yale Div school, UofC Div school, and Brandeis. We lived in Chicago before the masters, I wanted to be at Yale (with John Collins), but we still ended up at Harvard - only b/c my husband got offered a promotion in his current company if we moved to Boston. I don't regret it (although some schools tend to shy away from Harvard people) and loved working with Jon Levenson, Bernard Septimus, and Ellen Aitken (in early Christianity - she's now at McGill, which is where I'm headed this fall for my Ph.D.!) although I definitely missed the opportunity to work with Collins at Yale.
BTW, I'm wait-listed at NYU and finally got a negative from UofT's department of Near and Middle Eastern Civilizations. I also accepted the funding at McGill, so it looks like we're headed even further up north (much to my son's chagrin!).