THE WAY OF THORN AND THUNDER trilogy by Daniel Heath Justice
This trilogy speculatively re-imagines the Cherokee history of removal and relocation and redefines European fantastical tropes using Cherokee-centered imagery and worldviews.
GREEN GRASS, RUNNING WATER by Thomas King
One of the best books I've ever read: a funny, sad, gorgeous story that ties together a contemporary narrative about Indians living on Canada's prairies with slightly skewed creation myths and accounts of the historical horrors endured by First Nations people during the continent's European colonization.
A wry love story that also incorporates critiques of nuclear testing and dumping on Native lands.
EAST OF THE SUN AND WEST OF FORT SMITH by William Sanders
A collection of short stories from Sanders' entire career. You can see some of his best here, including the alternate history "The Undiscovered," in which a shanghaied, shipwrecked Shakespeare is trapped in 16th Century Appalachia and must stage his plays among the Cherokee, and the near-future "When the World is All on Fire" when climate change and toxic waste have caused Indian reservations to become prime property again.
Silko uses magical realism to chronicle numerous characters' journeys toward the prophetic, violent end of white dominance in the Americas.
TANTALIZE by Cynthia Leitich Smith
A departure from Smith's previous, realistic Indian YA stories, this YA novel jumps onto the vampire bandwagon, this time in a vampire-themed restaurant in Texas.
THE BONE WHISTLE by Eva Swan (Erzebet Yellowboy)
The Bone Whistle is about a woman who discovers her true heritage. She is the child of a wanaghi, one of the creatures of Native-American folklore.
A gothic young adult vampire story.
THE LESSER BLESSED by Richard Van Camp
A coming-of-age story of a native Canadian boy obsessed with Iron Maiden. Has elements of magical realism.
BEARHEART: THE HEIRSHIP CHRONICLES by Gerald Vizenor
Perhaps the first Native American science fiction, this is a journey through a dystopian future United States destroyed by the collapse of the fuel supply.
For more on the subject, see The Best Indian Books.