I have a similar commute, and I've been using some fleece-lined, waterproof shoe covers on my regular road shoes (SPD).
These are the ones that I have, and they're fantastic! I arrive at work with my toes still nice 'n' toasty.

I've been using them in temps with wind chills down in the tens (Fahrenheit), and I haven't had any issues. Any colder, and I can just add an extra pair of thin liner-type socks.