I can't definitively give you a top three and honestly don't see any value in ranking them like that. I would simply describe them as the ACLU for technology and the Internet in that they fight for general civil liberties. X and more specifically Elon Musk have shown that they are on the opposite side when it comes to many of those civil liberties even if they all agree on some other issues. Online censorship (both explicit and through algorithmic bias) is the most obvious example that bridges your two distinct groups. Musk might claim he agrees with the EFF on that, but through his and X's actions, it's clear he doesn't.