Yes.
As the spell states that the target takes bludgeoning damage equal to 1d6 + your spellcasting ability modifier rather than the stone does extra damage equal to 1d6 + your spellcasting ability modifier you can assume that the spell itself is causing the extra damage and not the stone.
Also note that you are using the stone as a ranged spell attack by throwing it or hurling it with a sling, so even with a sling, it's still a ranged spell attack.
This is important because most monster nonmagical immunities are worded something like the following two examples:
bludgeoning, piercing, and slashing from nonmagical weapons that
aren't silvered (Ice Devil, pg. 75 MM)
or
bludgeoning, piercing, and slashing from nonmagical weapons that
aren't adamantine (Iron Golem, pg. 170 MM)
As spells are NOT weapons unless stated, these two nonmagical immunities wouldn't protect against the extra damage caused by the spell.
Obviously, if the stone is used as a sling bullet, the normal damage from that attack probably shouldn't be considered magical.