This is very hard for me.
Not because I find it hard to come up with them, but I listen to 3 main genres of music, and within each are several subgenres. And within each, there are examples of pieces I consider to be masterpieces. And it would be impossible for me to consider the best of one genre or subgenre to be more worthy of being a masterpiece, than the best of another.
So, I will list several within each genre, but even this will be just a partial list.
Prog (symphonic, Zeuhl, avant-prog, Canterbury, prog-metal):
Yes - Gates of Delirium, Close to the Edge, Awaken
Genesis - Dancing Out With the Moolit Knight, almost the entirety of The Lamb Lies Down on Broardway
PFM - Per un Amico
Magma - Köhntarkösz Anteria, Mekanïk Destruktïw Kommandöh
Univers Zero - Jack the Ripper, Emanations
Banco - Io Sono Nato Libero
Il Balletto di Bronzo - YS
King Crimson - Larks' Tongues in Aspic part 1 and 2
Pain of Salvation - Remedy Lane
ELP - Tarkus
National Health - The Bryden 2-Step (for Amphibians) Part 1, part 2
Jazz (fusion, post-bop, avant-garde, chamber-jazz):
Mahavishnu Orchestra - Trilogy, Eternity's Breath
Return to Forever - The Duel of the Jester and the Tyrant, After the Cosmic Rain,
Allan Holdworth - The Un-Merry-Go- Round, Devil Take The Hindmost, Letters Of Marquee
John Coltrane - A Love Supreme
Steve Coleman's Natal Eclipse - Morphing
Steve Coleman and the 5 Elements - The Twelve Powers
Alice Coltrane - Isis and Osiris, Mantra
Anthony Braxton - Dk(Rhx) T U Gil-6 [Composition No. 40A],
John Abercrombie - Timeless
Classical (avant-garde, serial, 12 tone, atonal):
Elliot Carter - Variations for Orchestra, Three Illusions for Orchestra
Charles Wuorinen - 4th Piano Concerto, Iridule – 2006, for oboe and six players
Alban Berg - Violin Concerto
Joan Tower - Concerto for Orchestra, Silver Ladders
Bruno Maderna - 3rd Oboe Concerto
Ligeti - Ramifications, Violin Concerto
Bartok - Music for strings, percussion and celesta
Anna Þorvaldsdóttir (Thorvaldsdottir) - AIŌN