If you want to run clipless this looks like the best winter boot I have seen http://45nrth.com/products/category/softgoods

I have the shimano winter shoes and they help but are by no means perfect.

If you are running platform pedals I would just find some nice winter boots and maybe a couple layers of wool socks and that would work fine. The ones that cover your calf help a lot because it keeps the blood running into your feet warmer as well.