As most will agree, UPenn is an incredible school. The main limitation is that it's a program, rather than a school of public health. As a result, you may not have as diverse a set of research projects, course listings, or certificates to pursue. Nevertheless, you'll have access to a strong alumni network, career services office, and set of faculty. Since the program is also small, you have a chance for closer relationships with faculty. I think Philadelphia is okay for job/internship opportunities, but I may be wrong (don't know too much about the city).
Overall reputation aside, Emory is more established in the field of public health. I'm not going by the US News rankings or anything, but it being a school of public health rather than a program is naturally associated with a higher number of resources available for you. Pros include a ton of research projects, ability to customize coursework (ex: if you want to focus more on infectious disease epi), and the school's close ties with the CDC. For jobs and internships, Atlanta is probably more promising than Philadelphia.
It all boils down to your personal preference. Life in Philadelphia vs Atlanta is quite different. Being in a small vs large cohort is different as well. As many have said on here, what you do in the program ultimately matters more rather than where you go. Emory may have the bigger name in public health, but maybe UPenn is a better fit for you and your career goals. Either way, you have two very good schools to choose from.