NPR was, quite-literally created by an act of the United States congress.

It receives DIRECT funding from the United States government.

Twitter was generous in changing the label from "State-affiliated" media (given that it was literally created by the US Government) to "Government-funded media".

There is no possible argument against the "Government-funded media" label that makes sense. They're government funded. NPR's parent company, Corporation for Public Broadcasting, is also government funded. Neither of these funding points are debatable (aka Full stop).