The following are a few responses sent to the questioner.
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One of our volunteers put together a list of alternative libraries that might be of help (http://radicalreference.info/altlib_infoshop).
I know the Independent Publishing Resource Center (IPRC) in Portland, OR accepts donations. There's also a list of infoshops on http://infoshop.org.
Two other zine libraries that I know of are:
West Coast Zine Collection at San Diego State U. Library:
http://infodome.sdsu.edu/about/depts/spcollections/rarebooks/zinesfindingaid.shtml)
Barnard College zine collection:
http://www.barnard.edu/library/zines/
On the more commercial side, try Quimby's, an indy bookstore in Chicago that sells lots of zines. I'm not sure about their policy on purchasing zines, but it'd be worth it to contact them as well.
I hope this helps. Please let me know if you have further questions.
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You might also post to the Zine Librarians discussion list. If you don't feel like registering for the list, let me know.
I also recommend the ABC No Rio Zine Library, the San Francisco Public Library, and New York Public. There are lots of lists of zine libraries to mine for other possible collectors. One of my favorites is Zine Street, but there are many other worthy sites to be found with a search engine "zine libraries" query.
The academic and public libraries should pay for the zines, so I wouldn't bring up donating them at first. But for volunteer collections like ABC No Rio, an offer to donation the zine might help.
Good luck!