No it didn't. It originated from a lobbying group that *told them* something undesirable is happening. That lobbying group has a history of making blatantly antisemitic statements, and they claim to be representative of a community which has loudly and broadly disassociated themselves from them.
Then, like through a combination of "soft" bigotry and confirmation bias, badly misreported the story.
You give Yaffed too much credit if you really believe that they dictate what the NYT will cove,r.
Yes, Yaffed had been lobbying for investigation of yeshivas since 2015 (?). They continued in 2016, 2017, 2018 (when one of those yeshivas was found to be involved in fraud), 2019, and then, finally, in 2020, Shapiro and Rosenthal began their investigation. I don't interpret this as blindly following what Yaffed wants them to do.
I'm not defending their reporting, but I see it as slipshod more than malicious.