Sakura, like Tsunade, possesses unmatched physical striking power by focusing massive amounts of chakra into a single point. Therefore, Sakura's punches obviously carry more power than Naruto's. However, this is Sakura's only real offensive ability. She is essentially a tank. She can take huge amounts of damage, is slow, and has largely predictable attacks. Thus, while a single attack can kill a normal person, she rarely lands these blows properly, and therefore generally only causes superficial damage.
Naruto, on the other hand, is a much more versatile shinobi. He is able to compensate for this discrepancy in power by increasing his speed, using a Rasengan variation, infusing various Tailed Beast chakra, creating clones, etc.
Therefore, in this specific case, Naruto's attack is clearly more powerful. Sakura was able to catch Kaguya off guard and land a solid blow. This caused noticeable marks on her face, but only threw her back the opposite way a few feet if at all (it may have just caught her by surprise enough to prevent her from escaping). Naruto's attack was able to knock Kaguya back a considerable distance and break rocks on impact. We do not see an up close view of Kaguya to determine the level of damage, but Kaguya (still relatively fresh) seems shocked/dazed by the attack.
