Courtesy of Famitsu (So physical only) https://nintendoeverything.com/top-35-best-selling-switch-games-in-japan-four-years-in/

1. Animal Crossing: New Horizons – 6,625,026
2. Super Smash Bros. Ultimate – 4,145,903
3. Pokemon Sword/Shield – 3,955,554
4. Splatoon 2 – 3,771,338 
5. Mario Kart 8 Deluxe – 3,656,140
6. Ring Fit Adventure – 2,346,098
7. Super Mario Odyssey – 2,208,475
8. Momotaro Dentetsu: Showa, Heisei, Reiwa mo Teiban! – 1,846,039
9. Super Mario Party – 1,818,405
10. Minecraft – 1,806,925
11. Pokemon: Let’s Go, Pikachu / Eevee – 1,772,856
12. Zelda: Breath of the Wild – 1,771,235
13. Super Mario Maker 2 – 1,065,261
14. New Super Mario Bros. U Deluxe – 1,031,494
15. Kirby Star Allies – 878,800
16. Luigi’s Mansion 3 – 745,825
17. Clubhouse Games: 51 Worldwide Classics – 630,909
18. Taiko no Tatsujin: Drum ‘n’ Fun! – 572,215
19. Fishing Spirits Nintendo Switch Version – 566,909
20. Dragon Quest XI S – 560,075
21. Super Mario 3D All-Stars – 555,345
22. Pikmin 3 Deluxe – 536,209
23. 1-2 Switch – 483,430
24. Mario Tennis Aces – 479,866
25. ARMS – 461,056
26. Mario & Sonic at the Olympic Games Tokyo 2020 – 376,481
27. Dr. Kawashima’s Brain Training for Nintendo Switch – 363,759
28. Pokken Tournament DX – 344,201
29. Hyrule Warriors: Age of Calamity – 341,519
30. Fire Emblem: Three Houses – 323,562
31. Dragon Quest Builders 2 – 308,893
32. Paper Mario: The Origami King – 305,603
33. Yo-kai Watch 4 – 303,978
34. Zelda: Link’s Awakening – 300,027
35. eBaseball Powerful Pro Yakyuu 2020 – 284,876

Rise is about to enter the top 5.

Also wow... Dragon Quest seems like it would be a bit higher? I get its a late port, but. Then again, I think that digital was pretty strong in 2019 for boxed games.

Neat.

10 3rd party games (including Hyrule Warriors)

I know that it doesn't include digital, but based on physical sales, it is impressive that Splatoon 2 has outsold MK8DX, Odyssey & BOTW and comes within 500,000 of both SWSH & SSBU, despite those games trouncing Splatoon 2 worldwide. Splatoon 3 will definitely be a big hit in Japan (and worldwide).

If counting digital, do we know if ACNH has overtaken Pokemon RGB yet or is it currently in 2nd place? I'd imagine that it is close and will probably take it this year and become Japan's best selling game of all time.

Sources that I can find seem to differ on how much Pokemon RGB sold in Japan, but most seem to place it over 10 million, so AC is still #2 for now.

There are a whole lot of first party games on that list. That makes it extra impressive that Momotaro and Minecraft made it into the top 10.

There’s still a few more big games to come too.
Story of Seasons: Pioneers of Olive Town should have a few more big weeks to crack that 300,000 mark.
Bayonetta 3 should do similarly well.
Mario Golf and Monster Hunter Stories 2 could even be a little bit bigger and crack 400,000.

New Pokémon Snap will enter the top 20.
Skyward Sword should do similarly well in Japan.

Breath of the Wild 2 will sell over a million.
A Super Mario Party 2 would sell over a million.

Then there’s the mega blockbusters to come:
Monster Hunter Rise and Pokémon Diamond/Pearl will each do at least 2.5 million in Japan.
Pokémon Legends has the same potential.

Splatoon 3 will be even bigger than those games in Japan and should clear 3 million.

Then there’s the late gen blockbusters still to come like Pokémon Gen 9 and Dragon Quest XII that have 3 million+ potential.
Even little old Mario Kart would be guaranteed to sell 2.5 million in Japan if it happens.

Who knows what else could happen along the way and what surprise hits Japan will get?

Switch top 30 should compare very well to 3DS top by the end.

1. Pokémon X / Y – 4.504.626
2. Animal Crossing: New Leaf – 4.476.950
3. Pokémon Sun / Moon – 3.844.977
4. Monster Hunter 4 – 3.591.334
5. Yo-Kai Watch 2: Bony Spirits / Fleshy Souls – 3.210.295
6. Pokémon Omega Ruby / Alpha Sapphire – 3.170.976
7. Mario Kart 7 – 2.887.908
8. Monster Hunter Generations – 2.833.860
9. Yo-Kai Watch 2: Psychic Specters – 2.655.357
10. New Super Mario Bros. 2 – 2.624.127
11. Super Smash Bros. for Nintendo 3DS – 2.613.529
12. Monster Hunter 4 Ultimate – 2.571.350
13. Pokémon Ultra Sun / Ultra Moon – 2.529.930
14. Yo-Kai Watch Blasters – 2.191.034
15. Super Mario 3D Land – 2.178.637
16. Tomodachi Life – 1.826.729
17. Dragon Quest XI: Echoes of an Elusive Age – 1.817.915
18. Monster Hunter Generations Ultimate – 1.691.202
19. Monster Hunter 3 Ultimate – 1.589.804
20. Yo-Kai Watch 3: Sushi / Tempura – 1.516.996
21. Animal Crossing: Happy Home Designer – 1.507.126
22. Puzzle & Dragons Z – 1.477.621
23. Yo-Kai Watch – 1.303.281
24. Dragon Quest VII: Fragments of the Forgotten Past – 1.238.660
25. Super Mario Maker for Nintendo 3DS – 1.196.045
26. Luigi’s Mansion: Dark Moon – 1.057.454
27. Monster Strike – 999.955
28. Dragon Quest VIII: Journey of the Cursed King – 929.179
29. Dragon Quest Monsters: Terry’s Wonderland 3D – 921.310
30. Kirby Triple Deluxe – 851.295

Edit:

That does not even account for stronger digital sales on the Switch.

The sum of the Top 30 respectively is 46 Million(Switch) vs. 65 Million (3DS). So it's already 70% there without huge Monster Hunter or Dragon Quest games. And the Monster Hunter franchise alone did more than 12 Million on the 3DS. By the end of the Switch we could see the Top 30 getting close to 80+ Million.

I just realised that chart doesn’t include Super Mario 3D World + Bowser’s Fury yet.
That should be slotting in at 26th place with 422,000 units sold as of end of February.