Magic Stone says: "You or someone else can make a ranged spell attack with one of the pebbles by throwing it or hurling it with a sling. If thrown, it has a range of 60 feet. If someone else attacks with the pebble, that attacker adds your spellcasting ability modifier, not the attacker’s, to the attack roll. On a hit, the target takes bludgeoning damage equal to 1d6 + your spellcasting ability modifier."
Thrown Weapon Fighting says: "…when you hit with a ranged attack using a thrown weapon, you gain a +2 bonus to the damage roll."
It appears to me that throwing a Magic Stone is making a ranged attack with a thrown weapon. If so, should the damage on a hit be 1d6 + 2 + spellcasting ability modifier when thrown by someone with Thrown Weapon Fighting?
Best Answer
Rules as Written
With the rules as written, I'd say no. It is a ranged spell attack, not a thrown weapon attack. Especially since even if someone else throws the stone, they use your ability score modifier for the attack and damage roll.
Rules as Intended
Without a Sage Advice covering this, we can't say what RAI is for this situation.
Rules as Fun
By all means, go for it. Would the extra 2 points of damage unbalance the game in any way? I personally doubt it. Could it bring a combatant down one round earlier? Sure, but that's just going to make the combat more exciting.
Final Thoughts
If you're the DM, I generally advise rule in favor of the player when uncertain about something. If you're the player, you'll have to abide by what your DM rules.
Of course, we don't know the situation in which this question has arisen. Is it something a player has tried, or wants to try? Is it a tactic for a bad guy that your planning? I'd still say allow it in both situations. Just remember how it's ruled so it can be played the same way should the situation arise again.