For NYC specifically I've been burned many times by Citymapper. It is trying to be clever and parse the messages about service changes, but does it all wrong and in the end gives you wrong directions, leaving you stranded. Sometimes it doesn't show the alerts by MTA at all.
Now that the MTA app is so good and has achieved feature parity with Citymapper, I prefer that for 90% of the time. It doesn't have multi-modal (eg subway + citibike) and doesn't show estimates of uber/lyft prices, but those have not been very useful in my experience.
Citymapper is still ok to quickly check upcoming train or bus departures.
Now that the MTA app is so good and has achieved feature parity with Citymapper, I prefer that for 90% of the time. It doesn't have multi-modal (eg subway + citibike) and doesn't show estimates of uber/lyft prices, but those have not been very useful in my experience.
Citymapper is still ok to quickly check upcoming train or bus departures.