There's a whole bunch, is there something specific you're looking for? Just looking to walk in and catch live music of any kind? Want to see touring bands or random locals?
Usual go-tos I know of include the Horseshoe, Lee's Palace, Velvet Underground, (most nights) the Phoenix, the Garrison, the Opera House, etc. Also you could just look at
this list of tickets on sale to get a sense of popular venues in town. There are a lot of local venues not on that list that do mostly local bands, those I wouldn't know as much. If you're looking for jazz stuff, the Rex downtown always has someone playing (though I can't vouch for whether the Rex is actually good or not, feels a bit tourist-y). I know the Top of the Senator used to be a thing but I think that's gone now.