After having played almost every N64 game, i can say DOOM 64 is the best looking game.
Now bear with me. I know DOOM 64 is less ambitious than other, more advanced N64 games technically. But how many games can you say have aged well when playing them on original hardware? DOOM 64 is one of the very few games that do.
Almost all N64 games will suffer from some common N64 technical issue. It can be blurry textures, it can be heavy fog or it can be bad frame rate. Or it can be a combination of those three. Or all of them.
But DOOM 64 doesn't suffer from any of those. For starters, it's one of those very rare instances where some of the N64 VI filters are disabled, making it look sharper than average. It's textures are possibly the best/sharpest looking in the system because there is non of the usual low-res/stretching shenanigans here. The DOOM engine is pushed to it's limits, surpassing DOOM 2 on PC in complexity when all DOOM ports on other consoles had to use the simplified Jaguar DOOM levels. And the frame rate is perfect 30fps. There are no technical issues here other than being darker than it should.
As much as i love Goldeneye and Perfect Dark, these games are a struggle to play on original hardware nowadays. They are technically more advance, sure, but that gets ruined by all the blurriness and frame rate issues.
I think DOOM 64 strikes the perfect balance of frame rate and looks. Some other games come close, i would say Banjo-Kazooie has a nice balance (later RARE platform games have worse frame rate) and the later BOSS racers (WDC, Stunt Racer 64) are also great. But DOOM 64 has still aged better, visually, than those IMO.