If you're going to stick with clipless, consider some dedicated winter clipless shoes (Lake, Louis Garneau, Shimano, SIDI).

For commuting here in Colorado, I have a few different "grades" of shoe covers, the warmest being SealSkinz's heavy-duty oversocks. I just finished reviewing the Louis Garneau Bimax covers, and they're good for mild-moderate conditions. I tried some Shimano MTB winter shoes, but I couldn't replicate my preferred cleat position.