The best pop song of the 90s is more of a subjective question than an objective one, but we will go by sales, ratings, and popularity. The best thing that can possibly happen here is that you either re-find an old favorite song or you discover one you have never heard before. 
It may be feasible that you were either too young to enjoy the greatest pop artists of the 90s. It is also possible you were past the pop stage and now would like to find out what 90s music was all about.   
If you like hip-hop, you bought Hard Knock Life by Jay-Z. It would be almost impossible not to enjoy this song. And since it was so popular, it fits as pop. If you are a lover of alternative genre songs, you loved Losing My Religion by R.E.M. This song did not only sound good; it also has some deeper message, which is something you might want to explore if you did not interpret that meaning the initial time. 
Nothing compares to You by Sinead OConner was easily the best ballad of the decade. It really did make grown grown cry. You Oughta Know by Alanis Morissette once again proved how talented of a singer and songwriter Alanis can be. Unfortunately, she has not been motivated to do much since. And the best of the best was Smells Like Teen Spirit by Nirvana. 
This song changed the history of music and led to the death of hair bands. Smells Like Teen Spirit was a mega-hit. Check it out if you have not already.