Interesting circumstances each found themselves in. Janeway started out determined to uphold Starfleet protocols and philosophy in a wilderness and in the end found herself becoming a veritable Ripley (Alien), a mother wolf who would bend or break any rule or violate her own ethics in order to protect her brood.
Archer, meanwhile, similarly found himself in a wildnerness but had no paradigm from which to proceed except the Vulcan paradigm which he'd already largely rejected. He was forced to act as a pioneer in an ethical and tactical way, making it up as he went along. Given all that, I don't think he did the worst job. Too many people judge him against a future they already know but which he didn't.
Which was the better captain. Tough to say. I'd say overall (given his implied future) Archer was the more successful of the two. He did a very big thing while Janeway's accomplishment was much smaller... and don't tell me "she beat the Borg" because that was never implicitly stated or shown. She dealt them blow after blow, admittedly, but the foe remained after she brought her flock back to Earth.