Shameless (in-progress) plug:
https://yamtam.nycI find the NYC public transit system to be one of the most interesting in the world. Beyond the subways and LIRR and Metro North (which are covered by the MTA's app), there are literally dozens of other transit providers: Nassau bus, red bus, Suffolk bus, NJT, PATH, HBLR, Roosevelt Island Tram, and a shocking number of smaller targeted transit providers, as well as specialized transit modes like Citibike. No app, except maybe Citymapper, comes close to representing it all.
But Citymapper was acquired, by Via. A company who makes money when you don't choose public/mass transit. So that doesn't make me feel too good. Also, Citymapper doesn't work well offline.
Another important thing is that accessibility and alerts are regarded as very 2nd rate citizens on other apps, and for various reasons, I think these should be easier to see.
Enter my little tool. It has a long way to go, it doesn't do navigation very well (it's my own implementation of a weak algorithm), and doesn't work across modalities. But it does tell you the upcoming trains at stations (using the real time data), along with all the accessibility info, and alerts for the station and line. And links to complex maps, neighborhood maps, and more. And it can map schedules for the entire network 30 minutes into the future (2 hours for LIRR and Metro North), meaning you can go into airplane mode and it will keep working. Additionally, I have found it updates faster than other apps, as it is continually polling the MTA APIs.