We've known since Yoshio Sakamoto's pre-Other M press tour that Nintendo had offered some 3rd-party company the chance to make Metroid 64, but the company declined. According to an interview with games™, he stated that the company declined because they didn't feel confident in making a game that would compare favorably to Super Metroid. Regardless, to my knowledge, the company in question has never been revealed or confirmed (though Rare and DMA have been common suspects).

Anyhow, I was just chatting with a friend about the old (pre-2004) Super Metroid speedrunning and romhacking scene, and after exhausting some random small sites on the Wayback Machine I got to digging around on Google's Usenet Graveyard. I clicked on this thread because I thought the title was funny, and was met a few posts down with a revelation from some guy who claimed to be working at DMA Design. He said Nintendo had wanted them to turn their upcoming Body Harvest game into Metroid 64 (obviously they declined). A quick look at MobyGames shows that this man was indeed the Lead Artist on Body Harvest so, uh, this feels like a rather definitive answer.

I am barely able to contain mysdfklasl;khgladkjglkajsdhflkjahsdfl

EDIT: Clarity, added a link to the games™ interview