Mana is often more associated with magic in the sense of making something from nothingness, but Haki and Mana are both considered spiritual energy. They are interchangeable and used in much the same ways. To use a flying sword attack, for example, the swordsman must imbue their weapon with Haki.
The reason why Vegapunk will call it science in the fictional world is because it's pseudo-science in the real world. The normal world would call it magic because it's based on life force energy.
Mainly, this is an issue involving Western and Eastern beliefs. In the West, the logic of Devil Fruits and Haki would be considered magic. In the East, the logic of Devil Fruits and Haki is considered scientific. In other words, it's backward science based on esotericism. The modern world doesn't use this type of knowledge. Though, it is considered real by many people.