In my view, the most important factor to choose a PhD program is placement. In this aspect, Yale clearly dominates Penn, conditional on any field. Moreover, Yale PhD program is much more functional (better advising culture, funding, etc). Finally, I would say that Yale macro-growth group is as strong as Penn's.
I also got an offer from Penn this cycle, my interests are in business cycles/monetary theory/DSGE models (which is probably Penn's comparative advantage), but I wish I had an offer from Yale.