Regardless of what he does, Gore probably takes a fall, based on perceived guilt-by-association.
I totally disagree. I think
President Gore would have a much better chance of winning in 2000 than
candidate Gore did in OTL (and even
he almost won). (I assume that Clinton would only resign if there were a plea bargain keeping him out of prison, so no pardon would be required.) Journalists would gush about the "refreshing change" in the White House (Gore's "strong marriage" etc.) In OTL, Gore felt a great need to disassociate himself from Clinton in 2000--hence the choice of Lieberman (he may have helped a little with the Jewish vote, but he managed to lose a debate with Dick Cheney...); hence a populist "the people versus the powerful" campaign which really didn't suit a party holding the White House in a year of prosperity. He would not face that same pressure with a couple of years in the White House and his own record.
Monicagate did hurt Gore in OTL in 2000--not only (as I said) by making him choose a probably not-optimum campaign strategy, but also because, although voters opposed impeachment, they did show strong personal (though not job-performance) disapproval of Clinton, and this helped Bush with his claim he would "change the tone" in Washington. In this ATL, Gore would already have changed the tone for a couple of years, and Clinton having been out of office for a couple of years would be much less of an issue--while the peace and prosperity the US enjoyed under Clinton's administration would continue.
In other words, think of Gerald Ford in 1976 with no Reagan primary challenge (I don't think Gore will get a major one), no Nixon pardon [1], and a much better economy. (In November 1976, unemployment was at 7.8%, compared to 3.9% in November 2000.
https://fred.stlouisfed.org/data/UNRATE.txt) As it was, Ford almost beat Carter...
I have long been convinced that the Republicans in trying to drive Clinton from office and the Democrats in trying to keep him there--though acting understandably given the views of each party's base--were both acting against their party's interest, at least as far as the 2000 election was concerned.
(One other reason I am convinced Gore would win: he would not send Elian Gonzalez back to Cuba--he opposed the decision in OTL. I happen to think sending him back was the right thing to do but Florida's Cuban-Americans thought otherwise, and they did take it out on Gore despite his announced break with Clinton on that issue.)
[1] Even if I am wrong in thinking that Clinton would only resign if there were a plea bargain keeping him out of prison, I still don't see any pardon from Gore, precisely from the lesson of what had happened to Ford after the Nixon pardon.