Depends on what sites, as stated. Tofo is closer to Manta Reef and Giant's Castle, but Barra is closer to Amazon and Office. Those are some of the best dives in the area.
Tofo scuba is a good dive center. But they tend to have too large groups on their boats inmo. I have no experience from the others, but if I was going back I'd do a check to see if any of them offer diving in smaller groups – I'd be prepared to pay extra for that. There are no high end places in Tofo, I believe there is in Barra if that is what you're looking for. Casa Barry (don't confuse this with the location Barra) in Tofo has been the most popular alternative among divers, much because Tofo Scuba used to be located on their premises. They moved in november 06 and are now located on the other side of the village/beach.
cheers
Christian