In my humble opinion, a flute performance major candidate should focus more on the teacher than the school. Many fine music schools/departments may not have the teacher that is right for you. When working on a performance degree it is absolutely essential that you have a teacher who brings the best out of you; i.e., one with whom you really click. Many "big-name" flutists, unfortunately, do not make the best teacher. And it's not enough to choose a teacher by watching him or her work with others, for example, at a masterclass. In that setting, the flute "master" is not only working with you, but also those who are auditing. In my experience, some (and definitely not all) of these flute master class givers are highly charismatic in front of large audiences, but make for really lousy one-on-one teachers in the studio.
The best advice I could offer you is to find flutists you like who also teach at universities or conservatories. Try to set up a meeting, preferably even a short lesson, to see how the two of you click. Believe me, it would be a horrible situation if you saw someone you really liked at a masterclass, then went to study with them, only to find they are nothing in the studio like they are in big public surroundings. It's a sad reality in the flute world; but, unfortunately, it is true in some cases. Again -- I want to stress that not all are like that. And some flute professors are fantastic with certain types of students, but suck with others for some reason. But it happens more than you may think (bad match between professor and student). So the best way to protect yourself from possibly being stuck for 4 years with a teacher you don't like and, more importantly, one who does not inspire you, is to try your hardest to meet them inside the studio environment. You may have to pay for a lesson, but it would be worth it, in my opinion, considering the huge cost of possibly making a mistake in choosing a flute professor who was not the right one for you.
Go for the teacher, not the school. Also, bear in mind that some of these people teach at more than one college; that becomes important when evaluating cost because one of the places at which he or she teaches may be much less expensive than another (actually, that's exactly what I did; my graduate school teacher taught at 3 different places and I selected the school I could most afford; of course, you have to be able to get in to those schools, too

). And learn everything you possibly can about him or her. Talking to, or emailing, their former students (a google search easily turns up lots of flutists with web pages touting all of their teachers, so it's not hard to find them) is also a good tool to use.
Good luck!
SK