This sounds like possibly the 1972 Andre Norton novel A Breed to Come.
Points that match:
read around 1998, though I think it was written a few decades earlier
Check. Written in 1972.
Humanity had destroyed itself
Partial check. When desperate measures failed to control what men had begun and could not stop, they fled their polluted planet, leaving behind an epidemic virus born of experimentation.
and the characters in the story were all intelligent (and possibly humanoid, not sure) animals living in a community.
Check. Yet unlike men, whom the disease could destroy, the animals of the planet thrived. Each generation was more forceful and intelligent than the last.
Old technology (implied to be nuclear) was forbidden,
Partial check. In the ruins of what was once a university complex, a vast band of cats, more highly evolved than those on the outside, sought to master the works of men. But from what I remember reading it (has probably been 40 years or more) there was a lot of resistance to the small group that was trying to learn the technology
but for some reason it became necessary to travel along a river to a stash of technology. A big storm was an important part of the plot, though I'm not sure if it was just a threat or if it was the reason for the river trip in the first place.
Partial check. When humans come back to the planet the long simmering conflict between "The People" which are the feline derived humanoids and the "Ratons" evolved rats heats up, forcing a need to get even more technology.
A number of various covers exist. Perhaps one of these may match?