GTFS and GTFS-RT definitely work, but in practice it seems each transit agency implements them a little differently. I'm actually a fan of the HERE Transit API

GTFS and GTFS-RT definitely work, but in practice it seems each transit agency implements them a little differently. I'm actually a fan of the HERE Transit API. They've done the work of interfacing with a bunch of providers, and you can query their whole dataset with a REST API. Unfortunately it's proprietary and only free at small volumes. But I found it much easier to hook up than working directly with a transit agency. That said, their coverage can be a bit random. For example, I ended up having to do direct GTFS-RT anyway because HERE doesn't seem to have real-time data for NYC subways.