I think it is difficult to answer how many sub-species there are. I can't help you here. But maybe this paper is of interest to you:
Attard, Catherine RM, et al. "Hybridization of Southern Hemisphere blue whale subspecies and a sympatric area off Antarctica: impacts of whaling or climate change?." Molecular ecology 21.23 (2012): 5715-5727.
Within this one you might find cited papers which are of interest to you.
Currently are at least four subspecies of Balaenoptera musculus: the pygmy blue whale (brevicauda), the blue whale (Balaenoptera musculus musculus) and another two recognized "blue whales" (intermedia and indica). Are geographic stocks? The paper above mentioned by Schulz could elucidate this issue, But the commitee of Taxonomy of the SMM (Perrin) mentioned a new subspecies unnamed of Balaenoptera from South America.