I'm going to need some evidence on this.
Here's the end of year lists for eight publications in 1990. Some albums appear more often (Dee-Lite, LL Cool J, John Cale/Lou Reed), but to my eyes, about 75% of each list appears only once or twice.
NME:
# Pills 'n' thrills and bellyaches - Happy Mondays
# I do not want what I haven't got - Sinead O'Connor
# Fear of a black planet - Public enemy
# Ragged Glory - Neil Young & Crazy Horse
# Gold mother - James
# Behaviour - Pet shop boys
# People's Instinctive travels etc.. - A tribe called quest
# Floating - Julee Cruise
# Songs for drella - Lou Reed/John Cale
# World clique - Deee-lite
# Music from twin peaks - Angelo Badalmenti
# Goo - Sonic youth
# Nowhere - Ride
# Goodbye jumbo - World party
# Extricate - The fall
# The good son - Nick Cave
# The La's - The La's
# Bossanova - Pixies
# Reading, writing & arithmetic - The Sundays
# She hangs brightly - Mazzy star
The Face:
1. DEE-LITE World Clique
2. JULEE CRUISE Floating Into The Night
3. A TRIBE CALLED QUEST Peoples' Instinctive Travels In The Paths Of Rhythm
4. JUNGLE BROTHERS Done By The Force Of Nature
5. BELOVED Happiness
6. SOUL ll SOUL Vol 2 A New Decade
7. PET SHOP BOYS Behaviour
8. MONIE LOVE Down To Earth
9. HAPPY MONDAYS Pills 'N' Thrills And Bellyaches
10. BLAZE 25 Years Later
11. ANGELO BADALAMENTI Music From Twin Peaks
12. SINEAD O'CONNOR I Do Not Want What I Haven't Got
13. PUBLIC ENEMY Fear Of A Black Planet
14. THE SHAMEN En-Tact
15. LL COOL J Mama Said Knock You Out
16. TEN CITY State Of Mind
17. THE CHARLATANS Some Friendly
18. STEREO MCS Supernatural
19. ROBERT OWENS Rhythm's In Me
20. THE SUNDAYS Reading, Writing And Arithmetic
OOR:
1. LIVING COLOUR: Time’s Up
2. Neil YOUNG & CRAZY HORSE: Ragged Glory
3. WORLD PARTY: Goodbye Jumbo
4. The POGUES: Hell’s Ditch
5. PUBLIC ENEMY: Fear Of A Black Planet
6. Nick CAVE & THE BAD SEEDS: The Good Son
7. PIXIES: Bossanova
* Lou REED & John CALE: Songs For Drella
9. The SERENES: Barefoot & Pregnant
10. John HIATT: Stolen Moments
SPIN:
1. Ice Cube - AmeriKKKa's Most Wanted
2. Sonic Youth - Goo
3. Jane's Addiction - Ritual de lo Habitual
4. Alice In Chains - Facelift
5. Deee-Lite - World Clique
6. Neil Young - Ragged Glory
7. Teenage Fan Club - A Catholic Education
8. Public Enemy - Fear Of A Black Planet
9. Sinéad O'Connor - I Do Not Want What I Haven't Got
10. L.L. Cool J - Mama Said Knock You Out
11. Primus - Frizzle Fry
12. Bob Mould - Black Sheets Of Rain
13. The Breeders - Pod
14. Was (Not Was) - Are You OK?
15. Concrete Blonde - Bloodletting
16. Prince - Graffiti Bridge
17. Masters Of Reality - Masters Of Reality
18. Eric B. & Rakim - Let The Rhythm Hit 'Em
19. Lou Reed/John Cale - Songs For Drella
20. Soul II Soul - Vol II: 1990-A New Decade
Village Voice:
1. Neil Young - Ragged Glory
2. Sinéad O'Connor - I Do Not Want What I Haven't Got
3. Public Enemy - Fear Of A Black Planet
4. Sonic Youth - Goo
5. Living Colour - Time's Up
6. Ice Cube - AmeriKKKa's Most Wanted
7. Paul Simon - The Rhythm Of The Saints
8. Rosanne Cash - Interiors
9. LL Cool J - Mama Said Knock You Out
10. Prince - Graffiti Bridge
11. The Replacements - All Shook Down
12. The Chills - Submarine Bells
13. Deee-Lite - World Clique
14. Queen Latifah - All Hail The Queen
15. World Party - Goodbye Jumbo
16. Various Artists - Red Hot & Blue
17. Lou Reed/John Cale - Songs For Drella
18. A Tribe Called Quest - People's Instinctive Travels & The Paths Of Rhythm
19. Yo La Tengo - Fakebook
20. Los Lobos - The Neighbourhood
Sounds:
1. Pixies - Bossanova
2. Happy Mondays - Pills 'N' Thrills And Bellyaches
3. Nick Cave And The Bad Seeds - The Good Son
4. Mazzy Star - She Hangs Brightly
5. The Fall - Extricate
6. Public Enemy - Fear Of A Black Planet
7. Teenage Fanclub - A Catholic Education
8. Julee Cruise - Floating Into The Night
9. Cocteau Twins - Heaven Or Las Vegas
10. That Petrol Emotion - Chemicrazy
11. Dee-Lite - World Clique
12. New Fast Automatic Daffodils - Pigeonhole
13. Neil Young And Crazy Horse - Ragged Glory
14. Ride - Nowhere
15. The Heart Throbs - Cleopatra Grip
16. The Chills - Submarine Bells
17. Fugazi - Repeater
18. Sonic Youth - Goo
19. The La's - The La's
20. The Fatima Mansions - Viva Dead Ponies
Melody Maker:
# Pills 'n thrills and bellyaches - Happy Mondays
# World clique - Deee-lite
# Songs for drella - Lou Reed & John Cale
# Heaven or Las Vegas - Cocteau twins
# Ragged glory - Neil Young & Crazy horse
# Some friendly - The charlatans
# She hangs brightly - Mazzy star
# Ritual de lo habitual - Janes addiction
# Floating into the night - Julee Cruise
# Behaviour - The pet shop boys
# Bossanove - The pixies
# Fear of a black planet - Public enemy
# The la's - The la's
# I do not want what I hav'nt got - Sinead O'Connor
# The good son - Nick Cave
# Cleopatra grip - The heart throbs
# All shock down - The replacements
# Reading, writing and arithmetic - The Sundays
# Set the controls .. for the bass - Bass-o-matic
# Nowhere - Ride
Select:
# 1.Pixies - Bossanova
# 2.N.Cave & bad seeds - The good son
# 3.Depeche mode - Violator
# 4.Ride - Nowhere
# 5.Jane's addiction - Ritual de lo habitual
# 6.A tribe called quest - People's instinctive travel of path and rhythm
# 7.Galaxie 500 - This is our music
# =.N. Young & Crazy Horse - Ragged glory
# 9.Public Enemy - Fear of a black planet
# 10.Mazzy star - She hangs brightly
# 11.Dee-lite - World clique
# 12.Cocteau twins - Heaven or las vegas
# 13.Jungle brothers - Done by the forces of nature
# 14.Sined O'Connor - I do not want what I haven’t got
# 15.Chills - Submarine bells
# 16.Sonic youth - Goo
# 17.The fall - Extricate
# 18.Happy Mondays - Pills and thrills & bellyaches
# 19.Beloved - Happiness
# 20.Lou Reed & John Cale - Songs for drella
Interestingly, Daydream Nation didn't make number 1 on most of the music magazines in the UK in '88 - usually coming in between numbers 3 and 7.
EDIT: After some further research, I've discovered:
1990 - 67 unique artists across 8 best-of lists
2005 - 80 unique artists across 7 best-of lists
2006 - 68 unique artists across 7 best-of lists
From a mixture of mainstream and alternative publications - therefore, even the best-of lists of publications are becoming more diverse. Therefore, my own quote "end of year lists (where you could find them) were far more divergent, with very little overlap" doesn't hold true - the lists are as divergent as ever, regardless of source.