Hmmm this is a hard one for me, Slightly worrying that this is the hardest decision i have had to make all fortnight too!
first has to be Kirk, he is an iconic Captain, played his parts so well even if you discount all of TOS, his crossovers are all so character enriching and he just works, besides all his quirks and pet hates he works well.
picard is epic, his spin on whatever it is the writers had in mind is so unique and fitting you almost forget there was any other captain, that is unless you are a kirk fan.... janeway does her roll so well as the first female captain, groundbreaking and powerful she is my ideal leader in a female, voyagers story plays so well you feel comfortable with her in the chair.
Archer is a good captain, no scrap that a great captain, Enterprise is a very good trek series, so very strong in its own right and worthy of the trek name, love this show to bits and really am disappointed when trek fans dismiss it, great cast and great series only spoiled by a rushed hash of an ending.
And then there is DS9, great setting, great cast and great premise that is spoiled by a week captain, stale arc and to little to late war.
i enjoyed the series but it could have been so much more!