I second Lands of Red and Gold, it's not one I've actually read yet but it's one of the more well known TLs on this site and has a reputation for being very good
Doing a bit of looking into published fiction... A lot of indigenous-focused literature seems to be some combination of historical fiction, focused on natives of the Americas or Africa, more sci-fi focused (along the lines of afro- or indigenous- futurism, as opposed to a straight up alternate history along the lines of something like Flint's 1812/1824 books, Turtledove's TL-191, or most of the TLs on here. I'm kind of struggling to find much relating to the Aboriginals (and I'd probably have a harder time finding much at all about the Torres Strait Islanders) that isn't just straight up historical fiction.
There's Claire G. Coleman's
Terra Nullius, which sounds like something of an alternate history/speculative fiction (but not "hard alternate history") with a focus on Australia in the colonization period with both colonizer and aboriginal characters. From reading the reviews, it sounds like the reception of the writing itself is somewhat mixed (it is the author's first book), but the concept sounds neat and well-received (there's also something of a twist, so maybe stay clear of reading reviews if you don't want to be spoiled, if that matters to you). The writer is herself aboriginal, for what it's worth. She's also got a second book,
The Old Lie, which sounds like more of a straight up future sci fi, though it's apparently thematically focused as a sort of allegory for colonization or something along those lines
But otherwise, at least from my looking at various GoodReads book lists, it looks like the closest you'd get to alternate history with aboriginals doing better is something along the lines of future history, potentially with sci-fi and fantasy elements, with aboriginal main characters in settings where aboriginal society is somewhat better off compared to the rest of society relative to how things are in OTL, perhaps due to some sort of post apocalyptic setting where Aboriginal society is hit less hard and has a somewhat easier time recovering. But that's not exactly alternate history even if it is perhaps sort of close in terms of genre under the broader speculative fiction umbrella, so maybe that's just not of interest
Doing a bit more looking... There's
this page on uchronia.net, which is an entry for what looks like a rather straightforward alternate history scenario where aboriginals kind of do better, but... 1. It's just an entry page, the story itself was published in some magazine in 1992 so I don't know if you could even get your hands on it now, and 2. Well, reading the blurb for it, it sounds *really* implausible for a few reasons
Overall it doesn't look like there's a huge amount out there even if you are willing to widen your range considerably to speculative fiction outside of strict alternate history. TLs and discussion on this site are probably your best bet (with, again as said, Lands of Red and Gold being an exemplar example, but also with potentially some others that I haven't heard of)