Why are Japanese video games often rated the best?

Because the ones that we hear about are the ones that are good enough to have even made it out of Japan. If a game was bad, it wouldn't be localized to an English-speaking audience, and we wouldn't even know it exists.

It's the same sort of thinking as asking why (insert media here) was better in the past. The answer is simple - good songs, games, movies, etc. tend to be more memorable, and so we remember the good ones and forget the bad ones. To put it briefly, there's survivorship bias.

If you factor in every Japanese game in existence this statement will crumble really fast. Your examples are both Nintendo games and they have particularly high quality standards and a focus on fun gameplay (ignore the water temple in Ocarina of Time).

Those are both Nintendo, not merely 'Japanese'. However you may feel about Nintendo's legal proclivities, they are a longtime major player in the industry and, despite the gimmicky nature of the last few consoles, produce a very consistent, high quality with a brand perception in the ballpark of Disney. Those two things make them the default choice for any content-conscious parents or grandparents buying for kids, which has historically been the bulk of the market.

//edit: I guess that is half the explanation- the other half is the now large population of gamers with very warm, nostalgic feelings for Nintendo IP after the massive impact it had on their youth.

I'll play devil's avocado.

There are some genres that were effectively created by the Japanese gaming industry (Nintendo and others). Pokemon and monster hunting/battling. Final Fantasy/Dragon Quest and JRPGs. Hell, I'd even say visual novels (like Steins;Gate and others). Japan has been hugely successful at exporting these genres that were already domestically successful. And so they became the reference standards.

But if you were to look at racing games, or flight sims, or dozens (if not hundreds) of other categories, you'd see that they've failed to break into these genres with any significant effect. Not because they don't have the technical skills, but rather, they don't fall into their niche.

Cherry picking Mario and Zelda is unfair.

These are both nintendo and its more about wide appeal. I don't care for either myself.

Nintendo has been a dominant company in the video game industry for decades. It should come as no surprise that they've made some amazing games.

Because those games are better