That sounds implausibly high.

The disclaimer on the data says it's just an estimate, it's not from an official record, so I guess the real number isn't known.

I wonder why the real number isn't known.

Well it's not information that's collected by Harvard

It says there that the denominator (total number of graduate students) is 4577 when Wikipedia says it's 14,215.

While still greatly over-represented (https://news.ycombinator.com/item?id=23764422), Hillel tends to over-count Jewish students, according to https://ejewishphilanthropy.com/how-many-jewish-undergraduat...

That number is wildly inaccurate but even so, it's no doubt very different from the bad old days:

Certain private universities, most notably Harvard, introduced policies which effectively placed a quota on the number of Jews admitted to the university. According to historian David Oshinsky, on writing about Jonas Salk, "Most of the surrounding medical schools (Cornell, Columbia, Pennsylvania, and Yale) had rigid quotas in place. In 1935 Yale accepted 76 applicants from a pool of 501. About 200 of those applicants were Jewish and only five got in." He notes that Dean Milton Winternitz's instructions were remarkably precise: "Never admit more than five Jews, take only two Italian Catholics, and take no blacks at all."

https://en.wikipedia.org/wiki/Jewish_quota

If Jews are extremely over-represented (with respect to their share in the US population, which is about 1.7%), shouldn't there be an affirmative action for non-jewish students?

so this is saying Yale accepted 5 jews out of 76 students accepted overall. That's still a whopping 6% of all students accepted even though they make up < 2% of the population. How is that the bad?

Jews have always had it pretty good in the US, don't know what there really is to complain about.

That stat is worthless. They don't even define the population.