I seem to be one of those people whose feet won't stay warm while cycling without an active heat source. I tried chemical warmers a few times but they'd go cold less than half way through my commute due to oxygen starvation. Last year I used Hotronic e4 Nimh toe warmers which worked excellently.

They are quite expensive, I got mine during an end of season clearout. I recall someone posting info on similar product earlier in the year.

I also wear rain covers over my winter boots while riding which seems to help.