I don't know if they are "independent" enough for you but "world inferno friendship society" kicks more a** then an a@@ kicking machine. If you want to see a crazy live show they are worth checking out. They are based out of new york and play boston a good bit.
World/Inferno Friendship Society on MySpace Music - Free Streaming MP3s, Pictures & Music Downloads
Dave Tree's new band "SUPERPOWER" is a good punk/hardcore band that plays all around boston. I can't find there website or myspace for some reason.....
If you are into heavier stuff there is a band from Rhode Island called "Daughters" that tour around Boston and New York a good bit.
Daughters on MySpace Music - Free Streaming MP3s, Pictures & Music Downloads
anyway thats what I can think of off the top of my head if you could say what kind of music you dig I could narrow it down.