The list was probably based on rotation (and videos being picked from a hat by whoever that created the list) and that teen artists weren't taken seriously at the time.
Kylie Minogue's "Locomotion" was ranked at #87.
The Jets, Tiffany, and New Kids weren't listed.
"Smooth Criminal" was at 60 (a bit low...) though Taylor Dayne was nowhere on the list.
Oddly, Michael Bolton's "Sitting on the Dock of the Bay" was ranked at #88.

(MTV aired Bolton videos... :eek: )
#51 Bobby McFerrin "Don't Worry, Be Happy" (perhaps one of the worst songs ever)
Though there's some some songs/videos I'm not familiar with (may not be played often now, but might've been overplayed then...or whatever)...
LL Cool J "Going Back To Cali" and Rob Base & DJ EZ Rock "It Takes Two" were also popular and not on the countdown.
Though rap wasn't yet as popular in the mainstream (despite of the popularity of Run DMC, Beastie Boys, LL Cool J) and many probably still looked at as as a fad rather than another music genre. There's a few rap videos on the countdown and "Yo! MTV Raps" premiered that same year.