Class Ruling - Monk: Is a Monk's Ki "Magical"?

For the purpose of magic resistance: No.

"@JeremyECrawford Feb 23, 2016 Neither the Ki feature nor the Stunning Strike feature (PH, 78 & 79) is defined as magical for game purposes"

Unless a feature uses a spell slot or states "Magical", it is not.

House rule: A creature with advantage on saves from magical attacks does not have advantage against a Monk's stunning strike.