These programs have traditionally been considered very similar in reputation, quality of training, work-load, quality of residents, etc. One downside to the emory program is the geographic separation of their hospitals. As has previously been mentioned on this forum, the disaffiliation of baylor and methodist is not a big deal from the baylor IM dept. point of view.
I would say it's pretty much a toss up between the two and you should go with the one you liked the best when you visited