Either way works if you do it right. In color it is definitely easier for the reader to keep the characters straight-- face it, unless and until you really hook a reader, they _will_ think of your characters as 'short guy', 'elf guy', 'brown-haired girl', or what have you. particularly if your art skills are wobbly and/or you do a comic where people have more-or-less similar faces and few extremely distinguishing characteristics (horns, wings, one eye, beard, walrus teeth, etc), color can help determine who's who. if your art skills are good AND all your characters have very different faces and very consistent faces, it doesn't matter What color its in, people will know who's who. If you have an engaging storyline and characters that the reader cares about, it'll help as well, because people will make an extra effort to know whats going on. if they don't like the story etc, they'll speed through it (if they read it at all) and miss things.
no matter which you do, make sure the art is clean--sharp black lines, no grey except where you intend it to be, etc. Some sort of tone is recommendable too-- even if just solid black in places. a comic of thin outlines and no other tone is both boring and much easier to be confused about. it can work, but it will have to be that much better to outweigh the prejudice against the art.