The available data online are from actual league play, so it wouldn't be watered down by weaker barnstorming opponents. It is true that there was a smaller pool since there were fewer Blacks than Whites, but there is also a larger pool now compared to pre-integration. I think it's highly probable that the best Negro League players were as good as the best white players. If you look at the performance in the three decades after integration, half of the top 40 hitters by WAR were black players. I think it's safe to say that the superstars of the Negro Leagues would also have been superstars in the White leagues. You are right that you can't rank them precisely, but you can't really do that with different eras either.
Another thing is that the Black teams fared very well in head to head games versus white teams. You can say those were just exhibition games, but White MLB teams dominated White minor league teams at the same time. I think they would have liked to dominate the black teams too, but they couldn't. Yeah, there is still a lot of guess work, but the more I look at it, the more I think it's possible to come up with a reasonable ranking.