Oh, interesting! If I read the question strictly, I’m afraid I don’t have an answer. I think of Goosebumps as something for kids in grades 2-4, roughly, with a really light touch on genre elements and mostly a gently silly vibe. There’s not a ton of traditional SF written for middle-grade kids, and what little I know of is either fairly serious, or bad, or both. There are of course a ton of books I don’t know of, but I can’t speak to those.
If you expand out from a strict reading–if what you want is to get a kid a science-fiction novel that’s not YA material–I have two suggestions. Both of them are in Hyperion’s Rick Riordan Presents series.
Dragon Pearl is very much classic space opera, with the twist that it’s in a universe ruled by Korean folklore. A fox-spirit girl on a badly-terraformed planet runs away from home to unravel the mystery of her older brother’s disappearance. Along the way she fights space pirates, battles wits with a tiger-spirit spaceship captain, befriends a ghost and a goblin and a dragon, and gets into all sorts of hijinks. I read it with my third-graders sometimes with a lot of support.
Sal and Gabi Break the Universe is on my top five novels of all time, for kids and adults, and I read it with fifth graders, but younger kids could definitely appreciate it too. A Cuban-American boy whose mom died turns to stage magic as a way to handle his grief, and also can reach between parallel universes to pull things into his world, including his Mami Muerta. It’s a tremendously funny and bighearted book; after eight or nine readings it still makes me snort and giggle.
Oh! The Wild Robot is also worth considering. It’s extremely gentle, despite the scene where killer robots rampage across a wilderness island attacking woodland creatures and friendly robots alike.
Here are some series from a list that I give to my grandnephews and grandnieces. I have no idea how old your grandnieces are. Perhaps these are appropriate. If they are too hard as yet for them, give some of the series to them and tell them to put them on their bookshelves and wait till they are old enough if they find them to be too hard at the moment.:
L. M. Boston – The Green Knowe series
Edith Nesbit – The Psammead series
Daniel Pinkwater – The Snarkout Boys books
Daniel Pinkwater – The Mrs. Noodlekugel series
Joan Aiken – The Wolves of Willoughby Chase series
The list that I have of good children’s science fiction and fantasy series is very long. I decided to just include a few of those series. I’d include the whole Neddie & Friends series if I was going to recommend it. Here are the books in that series:
The first thing I check out if I can’t find a book I want at a local regular bookstore is https://www.abebooks.com/ . Chances are very good that they have inexpensive copies of the book you want in good condition. If you’re now choosing books for Christmas presents, order them immediately, because it will take a couple of weeks to get to you. If the book is out of copyright and even modestly well known, put the name of the book, the author, and the word Gutenberg into a browser to see if there’s a copy you can read online. (It’s a website called Project Gutenberg.) You could also go to YouTube and see if there’s a video with someone reading the book.