Well, 'The Magic School Bus' books were quite popular in the 90s. They had a science - fictiony feel as Ms. Frizzle took the kids on all kinds of wild adventures through time and space and into different scientific concepts. 'Redwall' by Brian Jacques, while not strictly science fiction, had some elements that could appeal to science - fiction - loving kids, like the epic battles and the detailed world - building. Also, 'The Chronicles of Narnia' which has been around for a while but was still popular in the 90s has some science - fiction - like elements such as different worlds and magical creatures.
Some great 90s children's science fiction books include 'The Giver' by Lois Lowry. It presents a dystopian society which is a common theme in science fiction. In this world, everything is controlled and a young boy named Jonas discovers the truth about his community. 'Holes' by Louis Sachar also has some science - fiction undertones. The story of Stanley Yelnats and his strange adventures at the Camp Green Lake has elements that make you think about time and fate. And then there's 'A Wrinkle in Time' by Madeleine L'Engle which is a classic of children's science fiction, taking kids on a journey through space and time to battle evil forces.