I assume you did some research before deciding where to apply. You can hardly go wrong with either school. As has been said many times before on many different threads, what matters most is what school you feel more drawn to. Medical schools are not going to care a whit between the two. See if these threads (a bit dated) help.
http://talk.collegeconfidential.com/stanford-university/615394-stanford-linguistics.html
http://talk.collegeconfidential.com/harvard-university/507174-linguistics-at-harvard.html