The publications of alternative presses/publishers would, by my definition, not be considered grey literature in that they have an independent publisher--an organization whose principal work is publishing has put the book or other material on the market. Grey lit is "published" by the organizations I mentioned-- federal, state, local government, corporations, and, as someone rightly added, ngo's--whose primary work or concern is not publishing, but who produce and distribute documents as a compliment to their main goals.
Having said that, I might add thank goodness for independent, alternative presses! They often maintain deep backlists as well as publish material that isn't considered commercially viable by larger concerns.