His connection to Epstein has been known since a long while before his stroke. He was asked about it numerous times and just deflected away from the question.

Epstein arranged several meetings in 2015 and 2016 with Mr. Chomsky, while he was a professor at the Massachusetts Institute of Technology. When asked about his relationship with Epstein, Mr. Chomsky replied in an email: “First response is that it is none of your business. Or anyone’s. Second is that I knew him and we met occasionally.” In March 2015, Epstein scheduled a gathering with Mr. Chomsky and Harvard University professor Martin Nowak and other academics, according to the documents. Mr. Chomsky said they had several meetings at Mr. Nowak’s research institute to discuss neuroscience and other topics. Two months later, Epstein planned to fly with Mr. Chomsky and his wife to have dinner with them and movie director Woody Allen and his wife, Soon-Yi Previn, the documents show. “If there was a flight, which I doubt, it would have been from Boston to New York, 30 minutes,” Mr. Chomsky said. “I’m unaware of the principle that requires that I inform you about an evening spent with a great artist.” Epstein donated at least $850,000 to MIT between 2002 and 2017, and more than $9.1 million to Harvard from 1998 to 2008, the schools have said. In 2021, Harvard said it was sanctioning Mr. Nowak for violating university policies in his dealings with Epstein, and was shutting a research center he ran that Epstein had funded. MIT said it was inappropriate to accept Epstein’s gifts, and that it later donated $850,000 to nonprofits supporting survivors of sexual abuse. In a 2020 interview with the “dunc tank” podcast, Mr. Chomsky said that people he considered worse than Epstein had donated to MIT. He didn’t mention any of his meetings with Epstein.

From WSJ

Keep in mind this is after Epstein was already known as a sex trafficker, the non-prosecution agreement was in 2008.