Complete speculation on my part but here goes.
Late 80s and most of the 90s everyone and their Mom was making sets of baseball cards. Add to that the fact that common base sets were in the 660-800 cards range. They produced in such mass quantity that they are so readily available after 20-30 years still in unopened form. Because the base sets were so big you have tons of cards very few care about. For every team star there was 20-30 other guys. I believe the strike effectively killed the interest of a lot of collectors as well. I know that is when I stopped the first time. You had everybody entering the card production market since it was so popular but then all of the sudden the strike happened and demand died. The overproduction of this timeframe exagerated the issue. A lack of huge named rookies in the timeframe could also play some role. There were certainly some, but not enough.
I believe basketball cards likely picked up some collectors in this timeframe. Even in the late 80s there were far fewer manufacturers for basketball cards. Hoops and Skybox came on late 80s to join Fleer and eventually others in the 90s. Other than a few sets in the early 90s where base sets were huge most of the sets were much more manageable. I think people have more name recognition with the typical role players in basketball than they do baseball as well. Fewer rookies and the fact that the 90s really had some great rookies classes to collect no doubt helped. Shaq, Garnett, Kidd, the great 96-97 class including Kobe, Iverson, Allen and many others on up to Duncan. In retrospect there is probably just a much better rate of desireable cards in those unopened boxes than there are in the baseball sets from the era.
My knowledge of basketball sets is limited and I don't know much about late 90s baseball since I was out of the hobby but those are some guesses. Switzr makes some good points as well.
