He's in the discussion, along with Jordan, Gretzky, Jim Brown -- people who are just head & shoulders above others in their sport. Big a T&F fan as I am, I can't think of any other T&F athletes who were just so much better than their competitors, especially not over a such long period. Maybe Nurmi.
Other people have brought up Bo Jackson, who was amazing but had his career(s) cut way too short to put him in the discussion.
I don't think it clear that Bolt is the greatest athlete of all time? He' certainly one of the greatest.
We need to define "athlete". Is the magnitude of athleticism required in sprinting (100m) anymore a display of athleticism than the athleticism required to dominate others at 10000M?
Is the best golfer in the world using superior athleticism to dominate golf?
Is the best marathoner in the world using superior athleticism to dominate marathoning?
Is the marathoner anymore athletic than the golfer in dominating his sport?
Is Bolt more athletic than Farah?
I agree with the above posts. It depends on the definition of "athlete," but I personally would put Bolt up there with others like Wilt Chamberlain and Michael Jordan, Bo Jackson, Gretzky and Lemieux, Jim Thorpe, Gebreselassie, Tiger Woods and Nicklaus, and Pele/either Ronaldo/whomever people think is the best footballer ever these days (I don't know much about it).
He's not definitively #1 by any means but with his obliteration of the WRs and unparalleled championship record he has to be in the conversation.