Nolan was probably the slightly better player when he was having a good year, but he was such an erratic player between injuries and inconsistent play that you really didn't know what you were going to get from one year to the next. His 1999-00 season was awesome ... but it was the only year in a four-year stretch dead in the middle of his prime where he cleared 50 points.
Amonte, by contrast, was a consistent, consistently healthy performer. You knew every year for a decade (save for the one off year under Keenan who didn't like him) you'd get a 35-goal sniper with a solid two-way game.
In this case if you could have one or the other in their prime for a season, I'd probably take the known quantity since the difference in peak values wasn't that high.