I think it depends on what you think you might want to do after your PhD. If you want to stay in academia then, at a topical level, Baylor has a stronger reputation for research. If not, then its important to look at what services the schools provide you with respect to career development. Apart from that, if the research fit is good for you at both places, think about which place you would be happier living in, and where you want to build your network.