Smith of Wootton Major . I read this book when I was about 10 or 11, and I still remember what it felt like as it rewired my mind.
Ender's Game, of course, as you'd said.
Scott Westerfeld's Leviathan trilogy (not to be confused with that other book by the same title).
Pretty much anything by Terry Pratchett except for The Colour of Magic (it's not great), but especially the Tiffany Aching books (starting with The Wee Free Men), and possibly Small Gods.
Neil Gaiman's Stardust, and especially The Dream Hunters.
The Myth series by Robert Asprin.
Hmm, upon reflecting on this list, I can see that it mostly consists of fantasy. I suspect this is due to my personal bias. I used to read science fiction exclusively when I was little, and there are tons of Russian science fiction writers whom I could recommend, if only your niece spoke Russian, which I suspect she does not. I was not aware that fantasy even existed until the aforementioned rewiring took place.
I bought my niece a Kindle that just arrived and I'm about to load it up with books to give it to her tomorrow for her birthday. I've decided to be a sneaky uncle and include good books that can teach better abilities to think or at least to consider science cool and interesting. She is currently in the 4th Grade with 5th coming after the Summer.
She reads basically at her own grade level so while I'm open to stuffing the Kindle with books to be read when she's ready, I'd like to focus on giving her books she can read now. Ender's Game will be on there most likely. Game of Thrones will not.
What books would you give a youngling? Her interests currently trend toward the young mystery section, Hardy Boys and the like, but in my experience she is very open to trying new books with particular interest in YA fantasy but not much interest in Sci Fi (if I'm doing any other optimizing this year, I'll try to change her opinion on Sci Fi).