We were the best Asian team during this time but we were not the world's best through the entire decade. When the 90s started, Pakistan was battling with West Indies for the number 1 spot. During this period, believe it or not, England were also a strong contender to be the best ODI side of the world.
Even though Australia were the world champion, they were a side who were considered strong but not the best. The mid 90s saw the rise of Sri Lanka and for a brief period, they were blowing everyone out of the water but Pak wrestled back the best Asian side title very soon. Saqlain & Afridi emerged as well as Akhtar which made our bowling really strong. Razzaq, Wasim, Moin, Azhar, & Afridi made Pakistan a really strong side as all of these were capable to ok batters who added a lot of balance to the side.
After dominating South Africa in the first half of the decade, the tables were turned and RSA had a 14 win streak against Pak in ODIs in the 90s. Australia also began their resurgence with Windies & England falling behind. The 90s ended with India also beginning to become more than a one-man side.
We may not be the best but we were throughout this decade one of the if not the most exciting side to watch. Saeed, Sohail, & Afridi were able to give quick starts. The middle order batters all had the potential to finish strongly while our pace and spin stocks were almost unmatched. There was no one like Wasim at that time, the likes of Starc or Johnson weren't there & the closest competitor to Wasim was Vaas who was slower & bowlers like Mullaly, & Zaheer Khan who didn't have the same pedigree.
This era, however, is also the darkest of our cricketing history. A deeper introspection or analysis ends up in murky places with Qayyum report highlighting some of the issues. At the end of the day, the 90s are a microcosm of Pakistani society as a whole; while one sees something of interest scattered here & there, if handled well it could have been magnificent but wasn't meant to be.