Just a correction... Bombinhas is in Santa Catarina, not Paraná. But I agree that this is indeed a very good point.
Well, not sure if this is what the OP meant, but south of Brazil comprehends the states of Paraná, Santa Catarina and Rio Grande do Sul.
I've never heard anything good about the dives (or if there is any) in Rio Grande do Sul, leaving us with only Santa Catarina and Parana.
Personnaly, I prefer Santa Catarina, where you can dive in the Ilha do Arvoredo (Arvoredo Island), either from Bombinhas or from Florianópolis (which is also the capital of Santa catarina).
Ilha do Arvoredo is a national park, and some points were closed for scuba diving, specially the ones closer to Bombinhas, so the boat trip is shorter if you go from Florianópolis.
As a side note, now is winter time there, so don't expect warm water/weather...
Cheers,
Rafael