Kirk is the man, no other Captain ever came close. The third season of ToS and some of the movies hurt the Kirk Character, but he's still the best.
Picard is still my number two guy, Stewart did wonders with him, at first he sucked, but as time went by, he became complex and interesting, as well as being compitent.
Sisko comes in a strong third, Brooks was superb, I loved the way DS9 stressed the father/son thing with him, and he was as good a war commander as trek has had.
Archer is next, Bakula has the potential to be the best, only the horrible writying prevents it.
Janeway makes me puke.