I work at a printing facility that puts out several papers a day, from a couple different companies. This is in upstate New York.
The Utica Observer-Dispatch, a Gatehouse Media paper, is NOT running these Doonesburys. I think they shy away from the controversial ones in general. We've been printing this paper less than a year, and from what I gathered from reading it, when they switched over the format when they started printing here (we print on paper that isn't as wide), they apparently moved Doonesbury to the opinion page.
The other papers are Gannett papers (owners of USA Today, among many others), and apparently it's up to the individual papers. The Elmira Star-Gazette and (Binghamton) Press and Sun-Bulletin are NOT running the regular strip, but the Ithaca Journal IS. This isn't surprising as Ithaca is home to Cornell University and is generally a leftie area, so likely would face less complaints. All 3 papers feature the strip on their opinion pages.
The replacement in the 3 using it is the week of Jeff/Red Rascal and Zonker's … nephew, I guess, sitting across from each other at a diner and using their smartphones the entire time, not talking to each other. I thought they'd just used those as reruns not long ago. (IIRC, the Gannett papers did run the Sarah Palin strips, but I think the Utica paper did not. There were also some other "controversial" strips that Utica didn't run, I think.) I don't think these papers offer comic strips on their websites, so there isn't that other option that I believe I read about.
The Guardian is running the strips unchanged in the UK, but then they were one of the few papers that ran the "Silent Scream" strips back in the eighties. Any other reports from the front line?