There truly is no comparison between the two. You really couldn't find two shows within the genre that are more dissimilar. Both are among my favorite television shows ever. If pressed, I may have to give the slight edge to Farscape. It had an element of fun that could sometimes be lacking from the deathly serious Babylon 5. The cast was also more consistent in quality (though Katsulas and Jurasik are both brilliant actors.)
Farscape's biggest strength could also be it's biggest weakness at times. It could sometimes go so completely off the wall, that it could make the viewer tune out. When Farscape was bad, it was very very bad. When it was good, though, it was some of the finest television ever made.