Sneak attack asks for a couple things, first you must hit with an attack. second that attack needs to be made with a finesse or ranged weapon. Third you need advantage or a enemy of the target within 5' of it to apply the extra damage.
So stones using a sling fits the criteria. Hitting with an attack, using a ranged weapon to make the attack (a sling) and the advantage or 5' thing are assumed in the situation, as without that you can't SA with anything.
In theory throwing the stones could still work as throwing a stone is an improvised weapon. Just because the attack is a spell attack doesn't change that a weapon is being used to make said spell attack. In this case RAW is a little more muddy than in most cases. If the rogue doesn't have proficiency with improvised weapons it would reason that they should take the penalty associated with not having proficiency on the attack.
