alt Hacker NewsI don't know about USA Today. NYT at least seems independent if left leaning. I've not seen them be unfairly biased or bend over backwards to cater to outside corporate interests just yet. They're certainly not bending the knee to the current administration.
They have a robust paying subscriber base that supports them and don't have an owner whose last name rhymes with Pesos who can axe a story just because he doesn't like what it says.
That a Democrat-leaning paper would criticize Republican politicians is not surprising. A better test of independence would be whether they criticize Democratic politicians (when they do things deserving criticism, that is: I don't expect them to criticize policy positions that they agree with, but all politicians do some things, in some cases many things, deserving of criticism).