Prost took on and beat Ayrton Senna in the same car. His overall list of teammates he competed against is significant and unmatched. Prost was essentially the king of the 1980s.
In my opinion that gives him the edge on Michael Schumacher. Suppose it depends on your criteria. Michael never taking on another champion in their prime, in the same car, or even a highly rated young star... I really count against him. The contrast there with Prost is significant.
In terms of ability... they're on a similar level. Hard to split them.
I think this is a bit harsh on Schumacher. After Senna's death there were zero world champions on the grid, and there wasn't a single driver with a reputation robust enough that if they became Schumacher's team-mate and subsequently failed, people wouldn't have been able to just say "Well they were rubbish anyway".
Herbert, Barrichello and Irvine were all highly rated young stars at some point in their career, and the dismissal of them now comes more as a result of how they did against Schumacher than anything they did before. For example, Johnny Herbert was a similar level to Hakkinen at Lotus, and beat everyone that came after. He then outqualified and finished ahead of the highly rated (by some anyway) Panis in a one-off drive at Ligier (where Panis had been all season) before joining Schumacher at Benetton.
And if you look at the drivers of that era that did subsequently go on to become champion (Hill, Villeneuve, Hakkinen), they were generally enjoying their primes at Williams/McLaren and joining Schumacher at Benetton/Ferrari is unlikely to have held any appeal to them.
But anyway, bringing this back round to Prost, I think I would put him behind both Senna and Schumacher overall. And getting back on topic, I think in addition to the races that have been mentioned, I don't think anyone has mentioned Kyalami 1982 where he came back to win after a puncture put him a lap down.