Is scarlet witch more powerful than thanos?
I'd argue in both the comics and the MCU, yes.
In the comics, she re-wrote reality to create another timeline in which Mutants were the superior race, collapsed that timeline, and deactivated the powers of millions of mutants at the same time when restoring original reality, and was able to temporarily destroy the Phoenix force, and leave its host intact.
In the movies, she was able to destroy the stone in Vision's head without assistance, and Thanos says that the only thing that's supposed to be able to destroy the stones is the stones themselves. Although in fairness, if I remember correctly, Age of Ultron says her powers were derived from the staff via experiments, so maybe that still holds true.