I don't recall the New York Times reporting a 90% chance of victory on election day. I recall her chances according to the Times decreasing several percentage points (down to the high 70s IIRC) during the last few days leading up to the election. If the interactive graphic you are talking about was the 'paths to victory' graphic that I'm thinking of, it probably reflected the most current polling data - which was probably already obsolete - that they had on hand at the moment.

My own observation during the days leading up to the election was that her chances of winning were decreasing at a faster rate than could be reported with reliable polling data, though I still believed that she'd eke out a win.