Marichal
Perry
Niekro
While I realize that just remaining in the Majors as a starter for 22 or 24 years is an accomplishment in and of itself, that doesn't really sway me when the question is "which of these three men was the best pitcher?"
Juan Marichal was the best pitcher. I look at things like Fielding Independent Pitching, strikeout to walk ratio, ERA +, WHIP, shutouts, etc. Marichal is best in all of them. Yes, the other two guys had their career metrics hurt by playing well past their prime, but when you compare their primes, Marichal was still the best.
First, the numbers. Their 10-year peaks:
While Niekro and Perry both had excellent numbers, overall, for their ten year primes, look at Marichal. He averaged 20 wins and 10 losses, a 2.65 ERA, and 194 strike outs a season for a decade.
Marichal has the lowest ERA, the best ERA +, the lowest WHIP by far, the best strikeout-to-walk ratio, and the most shutouts. His FIP is nearly identical to Perry's. Marichal's control was superior. Perry and Niekro hit twice as many batters, and their walk rates are substantially higher.
The stat that's most impressive to me is career shutouts. Niekro started 716 games in his career, and pitched 45 shutouts, or one per 16 (15.91) starts. Perry tossed 53 shutouts in 690 career starts, or one per 13 (13.01) starts. Look at Marichal, comparatively. He threw 52 shutouts in only 457 starts, or one per 9 (8.79) starts.
Then, look at how many times each man led the league in a particular metric.
Niekro in 22 seasons led the league in wins twice, ERA once, strikeouts once, and ERA + once.
Perry in 24 seasons led the league in wins three times, in ERA + once, in shutouts once, and in walks per 9 innings pitched once.
Marichal in 16 seasons led the league in wins twice, in ERA once, in shutouts twice, in ERA + twice, in WHIP twice, in hits per 9 innings once, in walks per 9 innings four times, and in strikeout to walk ratio three times.
I think it's clear Juan Marichal was not only in the class of Gaylord Perry and Phil Niekro, but he was better than either of them.