The joke was at the beginning--within the first 5 minutes--of season 5, episode 20, which first aired 18 December 1993.
The joke doesn't make any sense--to me, at least--but given that the MST3K reboot during the covid era--produced by Joel himself--was a gay woke-fest, you have to wonder. Maybe Joel knew something we didn't at the time.
Edit: It is a Mike Nelson episode. Immediately after the Epstein reference, Mike is ripping up a pair kid's underwear (briefs).
Dial up BBSes that catered to the 'unofficial' sort of communication and early usenet was full of Epstein discussions. Vague, at first - something about a skull and crossbones island where elites would go to rape kids. What they got right was the cannibalism and occult kabbalah rites.
This was late 80s and early-to-mid 90s.