The MTA. It is not perfect but it is good enough. I say this as someone who experienced Singapore and Japan's subway system.

My commute time is 30 - 45 mins and I pay $1100 for my room outside of Manhattan.

Centralized. Jobs are found either in midtown or downtown, and subway lines feed into both. Your commute will be dependent on how much you spend to be near work, but even a non expensive area (like eastern Bed Stuy or Crown Heights) doesn't have a commute more than 40-45m. You can also be lucky enough to be able to walk to work if you don't mind living in Manhattan, and spending more for a nearby neighborhood.