I like Citymapper's hybrid/multi-mode directions, such as taking the train to Citibike -- I like its Citibike support in general, it has a good real-time overlay. Citymapper also does a good job with nights/weekend subway closures.

I don't just use Citymapper, though. I also have Google Maps and Transit installed. I prefer Google Maps' subway overlay/general map. I only use Transit for nearby train/bus schedules.