How far is your commute? How much on segregated paths/lanes and how much in traffic?

In NYC your big enemy is wind so you want a good windbreaker up top and sometimes on the bottom. Most days when it's below about 30f I wear pretty much my regular clothes and believe strongly in KISS; sneakers, smartwool socks, jeans, UA base layer top, cotton mock turtle (lands end), sweater (depending on how cold it is), columbia ski jacket, good scarf, gloves, glasses (maui jims if sunny, tifossi yellow if overcast/night). I always carry an insulated headband for my ears (Dale or Columbia) though don't always wear it. If it's really cold I'll wear a ski hat (Columbia insulated) and I have some windbreaker pants I'll pull on over my jeans if it's really bad out.

The balaclava's a good idea. I just pull by scarf up over my face, but a balaclava would be better. I've also been known to stick a baggy over my toes before putting on my shoes.

Be careful not to let yourself overheat and sweat. You should be pretty cool starting out. As you warm up (Brooklyn or Manhattan bridge?), don't hesitate to unzip your jacket or pull your hat off for a bit.