I would say Shimokitazawa just west of Shibuya is a good place to go. I don't recall the exact names of the bars, but there quite a few very small but very local places out there. Maybe you ask some of the young people in the street or at another bar if you are looking for anything specific. Hope this helps. Enjoy!
As somebody who enjoys live music, I think Tokyo does offer interesting venues for live music. Even though many people might recommend bars or pubs with live music, I actually enjoy the street performances in Tokyo. In particular, it shouldn't be hard to find live band performances outside of Uneo station (and I really enjoyed it).