Urgh. 1999 was basically Vince Russo year. Crash TV to the max.
It's 1998 for me. The booking that year was great, especially in the main event scene. The main event scene was pretty dry after both Bret and Shawn left, leaving only Undertaker and Austin (who had only just become a main eventer) as the top guys, but they were clever and creative enough to craft a perfect main event that entire year. Austin/Vince, Austin/"Corporate" Dude Love, Austin/Kane, the "Are Undertaker and Kane are on the same side or not" storyline that carried them from the summer to the fall, the title being vacated, Austin being fired but then kidnapping Vince and being re-hired, the well-booked Deadly Games tournament where theoretically, any of four people could have possibly won it (Austin getting the belt back, Rock winning it because he had just become a baby face and his popularity was growing (he even beat Austin and Goldberg in a poll around that time), a freshly turned heel Undertaker, or Vince's corporate pick Mankind), and then Rock becoming a main eventer and corporate champion and feuding with Mankind while Vince tried to keep Austin from qualifying for the Royal Rumble match.
2000 is a close one, too. I feel that easily had the overall best roster of the AE years.