Technically, Sisko was Commander of Deep Space Nine, not Captain.

Unless you're talking about when he's on the Defiant. He's defo Captain of the Defiant.

Okay, pointless nerd aside over. Overall, I'm going to go with Janeway. Although, having said that, each of the Captains (and Commanders) definitely have their own areas of strength. Sisko is the best at being Space Jesus, for instance.