First, and most obviously, the NFL suspended Brady for four games, and he served that suspension. Did MLB ever take any action against Bonds? None I'm aware of. Last season he was the hitting coach for the Miami Marlins, and thus is obviously still able to work in baseball even after his retirement.
So the white guy was punished and the black guy was not.
Second, as to Brady, you certainly can't take the Wells Report as established fact. The NFL's selection of Wells to do the investigation was immediately denounced as unfair because he had previously worked for the NFL, which was perceived by many as being biased. After he issued his report, serious flaws were pointed out. One example is the analysis by a professor at MIT (yes, that's in the Boston area, but still). He examined the report's "findings" in terms of the established scientific principles and stated, "If I had to stake my reputation and my career on it, the Patriots balls match the Ideal Gas Law prediction, and I don't know why people can't get that." (The oversimplified version is that the balls were at the proper pressure when measured in the nice warm clubhouse, but the pressure dropped when the balls spent time in the cold. Remember that the game was played in New England in mid-January.)
Third, as to what the two players did: Even if you take the Wells Report as gospel truth, its conclusion as to Brady was that "it is more probable than not that Tom Brady was at least generally aware of the inappropriate activities of {two Patriots employees} involving the release of air from Patriots game balls {in the game against the Colts}." Even by Wells, the most he could say about Brady in the Colts game was the hedging "at least generally aware" language, and there was no finding of any impropriety in any other game. Bonds, by contrast, was using banned performance-enhancing drugs for the last several years of his playing career, and admitted to it, but alleged that his trainer had given him the drugs and had told him they were other (permitted) substances.
Furthermore, it's not exactly the case that Bonds "was not convicted of anything." The government wanted to nail BALCO Labs and Bonds's trainer, among other targets. To that end, Bonds was granted immunity so that he could be compelled to testify against them before the grand jury without taking the Fifth. He was then convicted of obstruction of justice for not testifying fully and honestly. The legal issue over which judges divided was whether his "rambling, non-responsive answer to a simple question" was enough to constitute obstruction of justice under the terms of the applicable criminal statute. The majority said that it was not, so his conviction was overturned. Whether or not his conduct on the stand was criminal, it was certainly wrongful, but of course he was never punished for that, either.
Finally, as to the "empirical factual advantage" of deflated balls, even the Wells Report admitted "that Brady's performance in the second half of the AFC Championship Game—after the Patriots game balls were re-inflated—improved as compared to his performance in the first half." There's certainly no question about the "empirical factual advantage" of using banned performance-enhancing drugs over a period of several years.
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