Per capita might not be fair.
Cities are not useful only for their inhabitants, they serve a function for the whole economy. Since resources are concentrated, value can be created more efficiently, economies of scale, and whatnot.
Another way of seeing it, is how much waste for NYC generate per dollar. It has a GDP over 1400 billion dollars.
This means that, if you were to get rid of NYC, because it's too wasteful, you would need around 4 or 5 large cities to replace the value it creates.
Probably, resource-wise, and waste-wise, nyc is not that inefficient, when you take into account, in your efficiency equation, that its value is much larger than hosting several million people.