I went to BU for my undergrad and Emory for my MPH. I have worked in the BU epi dept since and I would say go to Emory handsdown! While Atlanta isn't the best city in the world, its not a bad place to be as a student (its super cheap) and the Emory scene is great. Plus Emory is a phenomonal school, the classes are excellent and the teachers genuinely care about the success of their students. Its also really cool to be right next to the CDC which provides a lot of student job opportunities.
As far as BU goes, the professors at BU are very nice, but the program is less developed. Also, Boston is a lot more expensive than Atlanta, so its much less expensive to attend Emory than BU. I say go with Emory...just my 2 cents...