I really don't have a clue. I've been to Berlin two times now and i have to see that it is highly confusing and fragmented. But that is a good thing if you want to explore. All the touristy spots are obviously complete rubbish (parliament, kuh'damm, the historic sites, potsdammer Platz etc etc). Ok, perhaps not rubbish, buit it seems you're looking for a more eccentric experience.
There are also these quarters which once were very "alternative" but are now very gentrified e.g Prenzlauer Berg. But i think there is still a lot of "alternative culture" as in stereotypical leftwing/anarchist. One of these centers would be the "
köpi"...I hear its pretty famous.
Art...i don't know but remember the gallery Meredith Dittmar had an exhibition a while back:
http://www.strychnin.com Doesn't look too alternative i'm afraid...
What i found interesting was the contrast between east and west, which was still very noticable a couple of years ago. Perhaps things have changed now, but i would take the tram and just drive from west to east and notice the differences...
Sorry i can't be of more help, have fun
edit: Alright, i did some preliminary research....
http://reclaimyourcity.net/links