I've always gone with the Earth-colony idea and I've never been given any reason to change my mind. The idea that the nearest star system to us in the whole universe just happens to have a civilization of beings virtually indistinguishable from us is so contrived a coincidence that I've always found it distasteful. And it's based on a ridiculously literal and erroneous interpretation of the "Zefram Cochrane of Alpha Centauri" line from "Metamorphosis" -- which requires ignoring the preponderance of other
evidence from "Metamorphosis" proving unambiguously that Cochrane is an Earth human. (Cochrane asked if his visitors were "humans from Earth," he said his asteroid was "not Earth, but it's liveable," McCoy explicitly said he scanned as human, he was called human by Kirk, Spock, and Cochrane himself, he was initially distressed at the idea of a relationship with a nonhuman, etc.) So the idea was never anything more than an ill-considered mistake and I've never been the slightest bit inclined to believe it. And it hasn't been given any credence in the novels since the 1980s; even Judith & Garfield Reeves-Stevens, who were proponents of the native-Centaurian idea in Memory Prime
, had given it up in favor of the Earth-colony interpretation by the time they wrote Federation
And there's never been a trace of evidence for native Alpha Centaurians in canon. What little has been revealed about the system makes it pretty clear that it's a human colony. Obviously if Cochrane is an Earth human but "of Alpha Centauri," then humans must've colonized it in Cochrane's lifetime. ENT's depiction of Cochrane is consistent with this. "Twilight" also establishes that Alf Cen is a human colony (because it's one of the Xindi's targets in their campaign to exterminate humanity).
That said, in The Buried Age
, based on the real-life evidence that the Alpha Centauri system is 2 billion years older than Sol, I posited that there had been
native Centaurian civilizations in the remote past (at a time when the star was much more distant from Sol), but they hadn't survived long enough to reach the stars due to the frequent asteroid bombardments caused by Proxima Centauri's gravity disrupting the system's debris disk. Other than that, though, TBA makes it clear that Alf Cen is a human colony system through and through, so the question has already been answered within my own body of work.
ROTF:ACOF does contain a bit of discussion about the origins and history of the Alpha Centauri colony, and a few of its characters (though only one major one) are from there.