That would depend entirely on the specific details, including that 99% funding number. If you wanna allege specifics about NPR beyond "they once hired someone who used to work for the government", go for it.
So here's where we disagree: to me, any institution led by Medvedev won't be independent; funding formalities don't matter at all.
Also, once again: there's a fundamental difference between "used to work" and "was a CEO".
I'd be very skeptical of Medvedev, yes. The burden of proof for his independence would be... high.