Okay, I ran some calculations:
- 0Atk lvl 50 Emboar (Neutral) Fire Punch vs 0HP/0Def Mew (Neutral): 7% - 9% (25 - 31 HP). Guaranteed 14HKO.
- 12SpAtk lvl 50 Emboar (Neutral) Flamethrower vs 0HP/0SpDef Mew (Neutral): 8% - 9% (28 - 34 HP). Guaranteed 13HKO.
From these calcs, Flamethrower gives more damage. I tested them on a Mew, which has equal defensive stats. Emboar, at Level 50, has 143 Atk, which is why I used Level 50. The Level doesn't matter much here; I was aiming for your attack stat. Emboar's Special Attack reaches 120, so I added 12 EVs to make it 123, like your Emboar. Emboar's Flamethrower ends up doing a bit more due to the extra power it offers.
In conclusion, Flamethrower will do more. But I highly recommend that you use Fire Punch over Flamethrower, as Emboar's attack will increase quite fast due to its high base attack. Fire Punch also has more reliability.