famous one located in tehran, affiliated with university of tehran
dehkhoda institute/international center for persian studies
http://icps.ut.ac.ir/en/index.htminternationl students who come to university of tehran however attend another school specifically for learning farsi for academic study at the institution. its my understanding many universities which have sizable international student populations have their own in-house programs not open to short-term coursework.
as i recall, university of esfahan offered short term farsi courses to international students:
http://www.ui.ac.ir/isco/index.php#plcuijust try the web pages of major iranian universities. university web site info in iran, esp the english version pages, is usually pretty outdated. Find email addresses and phone numbers and get to work. A little effort and you should be able to get a hold of someone who knows about current programs in iran and the current status of successfully getting student visas for foreign nationals from a given country (e.g. america) for a given program.