There's no doubt that Agassi's 1999-early 2000 was peak Andre and that he probably never played better than in those 10 months. The other best players at this point, who played in that year's Master's Cup were Kafelnikov, Sampras, Enqvist, Kuerten, Kiefer, Lapentti and Todd Martin. Rafter and Moya were obviously big forces as they reached No1 that year but injuries meant they slipped from the top ranks.
I don't believe however, that Andre's hot streak comes anything close to Federer's 2004 or 2005 in terms of dominance. Andre won a mere 5 titles in 1999 and finished the year 64-14 I believe, and the Australian Open was his only title in 2000 I believe.