What makes you think Flannery O'Connor was the best? Flawlessly well-written stories and all very good. One limitation: frequently the same story. Deduct a point or two. Which ones are your favorites?
Personally, I think Edna O'Brien's The Love Object wipes the floor with nutty buddy if we're talking the best. But O'Connor is the rare writer, who as a stylist, almost never makes a mistake.
Oops, you said American story writer. Okay, if we take the average across all stories written you might be right. But the single best story always wins so I think it's someone else, maybe that Eudora Welty, Hortense Calisher, Salinger (Esme) or John O'Hara (the Doctor's Son). Their best (not their average) top O'Connor, who oddly is always close to her best in part because she mostly writes the same story