That funding page says 31% of NPR's revenue comes from programming fees from member stations. Some of the 8% "other revenues" and 5% "PRSS contract" sound like they may come from member stations too, so let's call it 40% total from member stations as a best guess.
Member stations themselves receive 13% of their revenue from the CPB (8%) and "federal, state, and local governments" (5%). Let's call that piece about 10% as a best guess of the federal-only part.
40% from member stations, which themselves get 10% from the Feds, is 4% additional from the Feds, bringing up NPR's federal revenue from the 1% they said to an all-in total of 5%.
It seems that NPR's statement is a bit misleading, but not that materially so.
(I'm as surprised as many of you may be, readers -- I thought they were much more federally funded as well.)
My accounting skills are less than amateur, so please point out anything I may have missed. I'm not quite sure if 40% of 10% computation is a sound representation of what's going on.