The extra damage is added to successful unarmed strike attacks, but not to the grapple's damage.
Per the Sage Advice Compendium's answer to "Can a monk use Stunning Strike with an unarmed strike, even though unarmed strikes aren’t weapons?":
The game often makes exceptions to general rules, and this is an important exception: that unarmed strikes count as melee weapon attacks despite not being weapons.
Hence, even if an unarmed strike does not count as a weapon the attack is still considered as a (melee) weapon attack, fulfilling the requirements for the Hunter's Mark spell.
On the other hand, the damage dealt to a grappled creature at the starting of the turn does not depend on an attack but it is automatically dealt, hence it can not benefit from the Hunter's Mark bonus.
You can find another part of the SAC which confirms this:
What does “melee weapon attack” mean: a melee attack with a weapon or an attack with a melee weapon?
It means a melee attack with a weapon. Similarly, “ranged weapon attack” means a ranged attack with a weapon. Some attacks count as a melee or ranged weapon attack even if a weapon isn’t involved, as specified in the text of those attacks. For example, an unarmed strike counts as a melee weapon attack, even though the attacker’s body isn’t considered a weapon.
Here’s a bit of wording minutia: we would write “melee-weapon attack” (with a hyphen) if we meant an attack with a melee weapon.