Commuting from Williamsburg to the Financial District via Ferry was more of a luxury when I did it rather than the most sensical means of transportation. Obviously, that's a different route than what you're asking, but I wouldn't imagine the experience is different. The ferries can become overcrowded during rush hour, especially coming home in the nice weather months. And if you're sensitive, there is a chance for motion sickness in choppy weather. Timewise, they can sometimes save you time, so long as your destinations are near the ferry landings.

The landings aren't very mass transit accessible in my experience. So unless you live/work right near the A and B of your trip, it might just be a warm-weather luxury for you as well.