I found one link about 'best animation degree programs',
http://talk.collegeconfidential.com/
However, if you want to be truly diligent, you will have to do some research of your own, such as, taking the animators you most admire and drilling down through the flotsam and jetsam and finding out where THEY got their degrees....
Most websites that list the ten best this or that are commercially motivated in some way and it would probably be better if you did your own research.
So, cough, get busy, and start looking at the resumes of successful animators. If you are really bold, you could even email these people and pitch them your story, as in I am looking to get a masters degree...and ask for some career advice. And then ask for an 'informational interview' meaning you go talk to them about their careers and you are NOT asking for a job...but you might get some good ideas and they might even refer you to someone else in the field.
Truthfully, do you really need a masters degree to get started in this field? I am just wondering....would a grunt level job in a successful studio be better? Or God forbid, an internship, called free employees? Joking, a little...
Good luck.