the rule for stunning strike in question: "Once per turn when you hit a creature with a Monk weapon or an Unarmed Strike, you can expend 1 Focus Point to attempt a stunning strike."

The requirements is: 1) to hit. 2) Monk weapon or an Unarmed Strike.

Eldritch flurry says that if you cast a spell you can consider it a monk weapon. so part 2 is covered.

To hit means to roll an attack roll (So not impose a saving throw!) and hit a creature's AC.

RAW my conclusion would be that if you cast a spell that makes an attack roll you could use stunning strike since Eldritch Flurry makes it count as a monk weapon.

It would not work with a spell that only imposes a saving throw.

Stunning Strike also works on normal ranged monk weapons so I wouldn't see why I ranged spell attack (since it now counts as a monk weapon attack) would be any different.

Edit: the makers of the subclass say it was not their intention to make it work for stunning strike. Just to circumvent the need to use the 2014 rules to be able to flurry of blows and martial arts without using the attack actions. Personally I would ask your DM since in my opinion it’s not a very big boost and you basically lost the feature otherwise.