El Ateneo is a chain of Bookstore. They own the most beautiful one in The Grand Splendid former theatre. It is a beautiful building and it is quite downtown. http://en.wikipedia.org/wiki/El_Ateneo
Nevertheless, it is a "mainstream" bookstore. You should go also to Corrientes corner with Callao to "Zivals" (also tango music, http://www.zivals.com/disqueria.html ) or "Ghandi" (Corrientes 1743)
In Palermo you can go to "La boutique del libro" (http://www.boutiquedellibro.com.ar/) which is also quite cool.
There are many in BA!!! about 4 years ago