Hmm, this is a tough one. They're both in the top 4-5. It's hard for me to give full credit to "The Slaver Weapon" since it's not an original story, but an adaptation of one of Larry Niven's Known Space novellas. It's good, but the original novella is better. I'm inclined to give more weight to "Pirates" because it's an original work, and not only that, but it was Howard Weinstein's first TV sale and he was 19 at the time, so it's impressive that it's so good. (Plus there's the fact that I know Howie personally, so maybe I should recuse myself anyway.)
"Slaver" definitely deserves note for being the only TAS episode where anyone dies in the course of the story, and one of the few episodes of any Filmation show where that happens. (I think there was an episode of Filmation's '66 Superman
where the evil aliens got blown up; there was an episode of the late-'70s Space Sentinels
where an elderly villainess died of old age on camera; the '79 Flash Gordon
had Hawkmen being disintegrated in flight; and the mid-'80s BraveStarr
, Filmation's last show, had three episodes featuring character deaths, treating it with far more weight and sense of tragedy than any of the prior instances.) It's interesting that they allowed Niven to adapt the ending intact rather than toning it down for Saturday morning.