With regard to Italian Americans and Sopranos, much of it is created by Italian Americans themselves. The tropes tend to be grounded in events from reallife history and have realistic context.
Also, stories about Italian American crime families never assume that every Italian American is a criminal. There are invariably examples of admirable Italian Americans, even in the same family, as well as the community at large. The goodguy Italian Americans are both informative, and a narrative contrast to heighten the strangeness of the criminality.
Perhaps a few shows are objectionable. But generally, the approach seems somewhat ideal, for how to go about exploring a darkside of a subculture.
I don't think you are accurately describing gangster movies.
1) Before the godfather a lot of media about the mafia wasn't made by or even starred Italian people. And there were plenty of mob movies after the Godfather, where the writers or the stars were not Italian (even in the Sopranos, some of the actors playing Italian mafioso are Jewish for example). And even in the Godfather a large bulk of the cast isn't Italian (including Brando himself who played the title role, and James Caan, who played Sonny).
2) A lot of negative tropes are grounded in real life events. That doesn't make associating Italian people with the mafia any potentially less negative (which is why there is a reliable minority of italian americans who decry Sopranos and games about the mafia).
3) I think your point that "stories about Italian American crime families never assume that every Italian American is a criminal", has a number of problems. For starters media featuring asian characters doesn't do this sort of thing either, but in both instances the genre tends to focus on the stereotype. But still, if you watch a movie like Goodfellas (which is my favorite of the lot), pretty much all the Italian characters in that film are involved in crime, associated with the mafia in some way, or benefiting from it). If one used movies like Goodfellas and The Godfather to form their understand of Italian Americans, it wouldn't be good. I think the position most of the pro-gangster film folk would take is that the Godfather and Goodfellas are not the problem, the problem is people thinking that a movie should form their understanding of something like that, or people who just think what they see in the movies is a model for real life.
This: "The goodguy Italian Americans are both informative, and a narrative contrast to heighten the strangeness of the criminality" simply isn't true. That is a trope from older gangster movies (you see it way more in films made by non-Italians where the gangsters needed to get their just deserts in the end for their bad behavior, or where the moral message of the film needed to be crystal clear. By the 70s though, you have a lot more moral gray. Who are the Italian good guys in the Godfather? Their people like Vito Corleone, who is still a mobster, still kills people, but just doesn't traffic narcotics (the bad Italians in that movie are trying to bring in the drug trade), and Michael Corleone, who kills his own brother in part 2. The first movie, and the book, basically just appropriates the war in heaven and Satan's fall, and brings it to a mobster landscape. But the 'good guys' are not at all your traditional good guys. And the same goes for a film like Goodfellas. Henry Hill is just the least sociopathic of the gangsters in that movie. The best thing we can say about him is he never actually kills anyone. But if you watch the movie enough, you also realize that he is an unreliable narrator and probably has in fact killed people (that is my reading at least at this point). And in the Sopranos even the good Italians are caught up in the criminal life of Tony and his crew. Artie Bucco isn't exactly someone to look up to (he is mostly depicted as a powerless and pathetic). The respectable Italians, like Tony's golfing buddies, are all snobs who find entertainment in things like mafia hits (which is why they even want to interact with Tony in the first place). When you are watching a gangster movie, you are there to get a glimpse into this strange and interesting underworld of criminals, and escape from the monotony of a more stable life. But you are not there to root for the good guys, and few viewers need the guy Italians in there to contrast with the bad ones.