I use Citymapper whenever I'm in NYC. In my experience, it's much better than Google Maps at providing alternate routes and predicting how long travel will take.

It also has many small touches that add up. My favorite ones are that Citymapper will tell you the optimal subway entrance to enter/exit and even which section of the train (front, middle, or back) to get on based on which one is closest to the exit in your destination stop.