I've commuted on my carbon road bike, my steel classic road bike, and two different Trek bonded aluminum MTBs, both converted to commuting use with rack, lights and slicks. It takes me an hour to commute on my MTB, it takes 59 minutes to commute on either road bike, it takes 55 minutes to commute by subway. In NYC there is no advantage to a road bike if you don't have long stretches of open road, and guess how much open road there is in NYC? Like none.
What do I usually use? My Trek 7000 MTB, now with fenders. I only wish I had a road bike when I get back to Prospect Park and want to do a few extra laps.