Generate stations.json using the offical MTA station list CSV #26
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The MTA does have listing of all stations in their dataset defined as "Station Locations" here
Every station is part of a Complex that can contain other stations. IE
Here you can see that Atlantic Av-Barclays Ctr has 3 rows, and the "Complex ID" is static accross all of them. This makes the station IDs consistent across all other MTA integrations as well.
http://web.mta.info/developers/developer-data-terms.html#data