In terms of the metrics, NYC is penalized for the following: temperature extremes, humidity extremes, tall buildings (plumbing, elevators, etc), and a number of other lesser factors.
NYC is benefitted by the fact that they don't grow anything, or really manufacture much.
NYC should strive to do better. Buildings should be better insulated, HVAC systems should be more efficient, heat recovery should be more widely used, lighting needs to be upgraded with more efficient solutions, and the subway should really try to improve efficiency.
But all these best and worst rankings are bunk without proper context.