I listen to a lot of progressive and avant-garde music, so a huge part of my collection is by bands, musicians, composers that are not popular.
Of course I listen to most of the better known prog bands: Yes, Genesis, ELP, King Crimson, Steve Wilson, Riverside, etc. But the great thing about prog and its associated subgenres, is that popularity is almost completely unrelated to quality.
None of these is 'the best', since, for me, they are all so good, it is hard to rate one over another.
This is a very short prog only list, I could make similar lists for jazz, and modern and contemporary classical, too.
Eskaton - 4 Visions (1981) / French progressive band, with this brilliant album of beauty, intensity, emotion, and incredible musicianship.
Thinking Plague - In Extremis (1998) / US band with one of the best examples of avant-prog. Atonal, dissonant, creative. Amazing musicianship.
Arti e Mestieri - Tilt (1974) / Italian band that straddles the line between jazz-rock fusion and prog. There are more great melodies on this one album, than many bands compose in a lifetime. And the drummer, Furio Chirrico, is an absolute beast, who belongs in the same class as Billy Cobham or Lenny White.
The Contortionist - Language (2014) / US technical-metal band, loaded with emotion, and chops from hell. Very complex.
Echolyn - As The World (1995) / US prog band, with great, complex multi-part vocals (in the Gentle Giant vein). Great melodies, playing, complexity all over this recording. And it rocks!
Discus - Tot Licht (2003) / Indonesian band that bends Mahavishnu Orchestra style fusion, Indonesian Gamelan percussion, prog, and contemporary classical, and somehow make it work. Very unique. The leader, guitarist Iwan Hasan, has major chops.
I could go on for pages...