So torn, but I think I'm going with Janeway. I loved watching her struggle mightily with the decision to keep heading home instead of giving up and settling down in the Delta Quadrant, even when her crew seemed ready to mutiny over it. She sought input from all her staff, but the decision was always hers, and she took full responsibility for it, even when it didn't go all that well.
Now these are things all the captains did, I suppose, but with Janeway, she wasn't afraid to let her guard down. She had real feelings, and actually expressed them from time to time. She also didn't have any problems showing the people around her how much she cared for them, even when she had to switch gears and be a hardass to them. Out of all the series, theirs truly was the most of a family, since they were all stuck together on the same ship for years on end with zero other people of their own race to interact with. She was tough *and* tender, compassionate *and* stern, and held that balance with a lot of heart and strength.
In some ways, I liked Sisko for the same reasons - he was a hell of a leader and demanded the best from his people and got it because of the respect he earned. Sometimes, though, when he finally got around to expressing himself, it came off as "the dam has finally burst" dramatic.
Picard and Kirk? Apples and oranges, and both were tremendous in their own ways.
And Archer? I actually liked Archer, but I didn't have enough appreciation for the series to really appreciate him as a captain.