HAL Laboratories when they made Melee.
Of those two probably Rare with DKC 1 and 2, definitely most impressive for it's time.

Nothing Retro has ever released is as good as Rare's Snes run imo, so i have to go Rare.

Rare's N64 games aged horribly for the most part, so their peak was a narrow band betwen DKC and DKC2 really.

Difficult question! The game I love the most from these two companies is Metroid Prime. But when I look at Rare during their N64 days, which were clearly their peak, I just have to give it to them. Their N64 output + Starfox Adventures includes many, many gems. Retro sure had higher dev costs, but I'm also sure Rare would have produced a lot more than two games (Prime 1 + 2) during the GameCube days.

Retro's peak was from roughly 2002 to 2014, when they released roughly one game every three years. None of their later games lived up to Metroid Prime's reception, but they were still batting around 90 on Metacritic on average.

Rare is a bit hard to directly compare both due to the smaller scale of game development during their 1994 to 2001 peak, along with the number of smaller projects they made. Not to mention that Metacritic doesn't go far back enough to cover all of their notable works. Still, of their 11 N64 games, 8 had a Metascore of at least 85. Looking at the top rated SNES games on GameFAQs, the entire DKC trilogy is there. And on the Game Boy and GBC, you have 2 and 4 games in their respective Top 50's for the platform.

That's a total of roughly 17 good-to-great games released over an 8 year period. Even pre-2000, that is a level of output only rarely ever seen. The average Retro game was probably better, but Rare's best games were roughly as good and much more frequent.

EDIT: The only devs I can think of with a better output would be Square circa 1991 to 2002. They were putting out roughly 2 or 3 all-time classics per year.

Imho, Rare by a very long shot!
DK 1~3 was like black magic on Snes.
Bajo kazooie, Conkers, Perfect Dark, 007... all legendary games. Rare at its peak can, almost, rival the best years of Nintendo. Retro doesn't even come close.

Rare by a long shot. The only difference is that Retro has not stooped as low as Rare has at any point, and has been far more consistent. They have also been able to keep Rare IPs (Donkey Kong Country) current and fun - even if not quite reaching the levels of DKC1 and DKC2. Rare had its moment during SNES and N64 eras, but was already declining by the time of Jet Force Gemini. Retro, on the other hand, had both the best game in the comparison (Metroid Prime) and have remained a very good group (Metroid Prime 4 is unfairly criticized - yes it is less good than 1 and 2, but not a poor game). In other words, while Rare was better when things were good, I would take Retro now any day.

Banjo, GoldenEye, and Perfect Dark were quite revolutionary for their time. I’d argue Banjo mastered the collect-a-thon/platformer gameplay loop, and stands toe-to-toe with titans such as Mario 64.

Also to answer OP: I struggle to see how one could even compare the studio behind MP Trilogy and DKCReturns with DKCountry Trilogy, Banjo Kazooie/Twoie, Goldeneye/PD, Conker, SFAdventures, Diddy Kong Racing, etc. There were more highs, and the highs were significantly higher: DKCReturns built upon the foundations laid out in Rare’s DKC Trilogy, MP built upon the foundations laid out in Rare’s GE007 and Perfect Dark. Rare pushed the industry so much further forward than Retro could even dream— Silicon Graphics, how to make a first-person shooter, perfecting the collect-a-thon genre, even mastered the Zelda formula in SFAdventures IMO.

I actually think their peaks are fairly comparable; for my money, Metroid Prime 1 is one of the finest video games ever crafted and can stand toe to toe with the absolute best Rare ever made, and Prime 2 + 3/Tropical Freeze are as great as most of Rare's classics.

Rare were more prolific and broke more ground, but that's not really a fair comparison as it was far easier to do that in the 90s than it was from the 2000s onwards when there was less ground left to break and games took longer to make.