To the best of my knowledge, no program specifically concentrates on Alternative photography. However, they may have a few classes over the course of multiple semesters regarding that.
Here in India we have GOA-CAP (GOA Centre for Alternative Photography)
They have a number of paid residencies and an annual sponsored one. They practice quite a bit of alternative processes (albumen, gum bichromate, C type, Salt Prints etc)
Here are some links that might help you
http://goa-cap.com/
And this is the blog that the residents maintain.
http://altlab2011.wordpress.com/2012/12/25/altlab-3-0
If you need more information, feel free to hit me up.
cheers!