As I think of good candidates for this I’ll try to add some here, if you like?
One place that I think has been consistent is ProPublica. Since they’re a nonprofit, one of the good things they can do that other places can’t is to pursue important stories that don’t have viral qualities - things everybody needs to know about, that contribute to public knowledge and fulfill the watchdog component of journalism but won’t necessarily get a lot of buzz.
There are other mainstream and internet organizations that sometimes do good investigative work but also have problems, so I have a hard time unequivocally saying “this is a good place, you should definitely support them,” like the New York Times, the Guardian, Buzzfeed, Huffington Post (occasionally), The Intercept, etc.
I think The Appeal has done some good “criminal justice”-focused stuff.
There are a lot of legacy magazines who I think are compromised to varying extents by their elite status (of the editors, reporters and the general reputation of the magazine). So for example I think the New Yorker and Harper’s still put out good investigative pieces, but I would probably look at the author and judge accordingly, or read the story but with some skepticism. The New York Times fits here also, I think.
The Atlantic is a similar elite magazine with a liberal reputation and still has a couple of very good writers working there, but I think under the current editor has taken a severe rightward turn and published several extremely trolly supposedly liberal but in fact right wing pieces, such as an extremely specious and problematic transphobic cover story. The current editor in chief attempted to hire Kevin Williamson, who you can Google, until blowback got so severe that they rescinded the hire. They also now have Rahm Emmanuel as a contributing editor, fresh from his ugly career as a truly dreadful mayor of Chicago, where he spent a year covering up a police killing. So I have a couple of writers there who I would want to read, but ignore the rest of it. I could go on but I won’t.
One group that has consistently done good work in a tightly focused area is Unicorn Riot. It’s pretty interesting because they claim to be decentralized and non-hierarchical collective It’s funded by donations and grants. They’ve focused heavily on antifascist reporting - they’ve done a lot of Discord leaks but also gone through the leaks to contextualize them summarize their findings. Looking at their website now, I see they’ve broadened a lot and are doing reporting under a number of topics. I would like to see this model spread, actually - non-hierarchical decentralized news orgs. I think if anyone wants to start one it would probably be best to start with an extremely tight focus and broaden out as you get more people with broader expertise, but you’d have to ask someone from UR about their experiences and what they think.
In a similar vein there is It’s Going Down, an explicitly anarchist news collective. I’m not sure they do much deeper investigative work, but I could be wrong. Also - they have a weekly radio show on KPFA now???