Perhaps the most remarkable "prediction" ... is Trump as US president (made in 2000!).
That is indeed a pretty impressive prediction, but it is less outlandish than you are probably aware. In regard to this prediction, it is worth bearing in mind that even by 2000, Trump had established himself as a popular business figure in the USA, and had made well-known forays in entertainment and politics, including an aborted presidential run. During the 1980-90s Trump had made regular forays into political issues and published various newspaper advertisements setting out his views on foreign policy and crime control. In 1999 he sought candidacy as the Presidential nominee for the Reform Party of the USA, but he withdrew from his attempted candidacy in February 2000, citing problems with the party. He indicated that he might run for President in a future election.
Trump was one of the most admired business figures of the 1980-90s. He had made a successful career in New-York real-estate and also commonly featured in popular culture (e.g., in a bit part as himself in the 1992 movie Home Alone II). He was regularly interviewed in the media in relation to political and social issues in New York. In September 1987 he published a major advertisement in multiple newspapers advertising his foreign policy views (see e.g., this NYT article). His spokesman told the media, "There is absolutely no plan to run for mayor, governor or United States senator. He will not comment about the Presidency." In 1989, during a period of high crime in New York, he published another advertisement calling for reinstatement of the death penalty and increases in police. In a 1989 Gallup poll he was listed as the tenth most admired man in America.
Aside from The Simpsons there have been various other items of popular entertainment that featured Trump in his aspirations for the presidency at around the same time. The video clip for the 1999 Rage Against the Machine song "Sleep Now in the Fire" shows the band holding a concert on Wall Street, with a mixture of head-bangers and bankers, and they show one of the bankers holding up a sign promoting Trump's 2000 presidential run (at 1:04 min).
The episode of The Simpsons that you are referring to would probably have been written during the run-up to the 2000 presidential election, and so the writers would have been aware that Trump was a candidate for a minor party. It is likely that the episode was making fun of the fact that he was (at that stage) an outside candidate for a minor party, who had some populist support, but was unlikely to win. Trump's aborted candidacy for President in 2000 foreshadowed his later runs, and even when he withdrew from that attempt, he indicated that he might run again. In January 2000, prior to withdrawing from his presidential run, he released his political book, "The America We Deserve".
I suspect that this episode of The Simpsons was just poking a bit of fun at a possible future with a populist candidate who was running for a small party. However, even back then, it was not a stretch to imagine that Trump would run again for the presidency. It is certainly an impressive prediction, but less so if you know the history of Trump in politics.