I agree with the others that either way it's a good choice. Vanderbilt might have a slight edge due to its renowned faculty members, nih money... etc... Emory does not fall short either. Just last year Emory received 261 million from Coca Cola.. I'm sure Emory has a ton of NIH money too... From what I heard from Emory students, Emory ranks in the top 5 in terms of endowment. If you've ever been to Emory long enough, you'll definitely know that money is definitely not something that the school has to worry about... which is a good thing.
However, from comparing both schools, I find that Emory definitely has unique characteristics that allows for students to explore different areas of medicine rather than just focusing on either academic, primary care, or specialties. For example, if you're interested in international health, you can easily get a mph degree or do research at the CDC. Futher from reading what desidr posted in an earlier thread they want to strenghten the international emphasis with this new curriculum. If international health is something you're interested in then Emory would be a great place for you to explore those options. If your interests lies in research, there are plenty of opportunities for you to do that too: Yerkes, Woodruff health Sciences resarch Lab, white head, cutting edge chemistry research (they invented the new HIV drug Emtriva).
Also, set to happen in the next 5-10 years, Emory University is going to rebuild their medical complex. What this probably means is better facilities and the need for more academics (possibly world renowned ones too). Thus, in my opinion Emory will catch up to other schools in the very near future.