From the research I've done when looking for a college my advice is to go somewhere with good theater/acting classes and apply what you learn there to your hand. I'm attempting to minor in thatm while getting a visual art major that I can use toward film. I think of puppetry as a mixture of dramatic and visual arts, so dividing my major and minor up that way I think I'll learn a lot. Also, doing my own homework on puppetry makes it more important to me, and experience is definitely the best teacher in this area, so I've started a puppeteering group on my campus and hope to do some filming before the quarter's out.
I was fortunate to get to have lunch with Leo Brodie this Tuesday, and he told me that he majored in theater and had got to do a workshop with JHC and then started his own company in LA with other pro puppeteers. It doesn't say anything about colleges as far as I can recall, but his website does prove that you can go pretty far with a theater degree and trial and error:
www.punchandbrodie.com
Good Providence to ya!