Is she perceived that way? By whom? Your question right now boils down to "Why do I perceive Queen Nefertiti as the most powerful female figure of Ancient Egypt?" Her popular fame likely has a lot to do with the discovery of her tomb.

Nefertiti was the wife of Akhenaten, the father of Tutankhamun. She is one of the most famous female figures of Ancient Egypt, due to the fact that her husband was the famous "heretic" who attempted to make Egypt follow a monotheistic religion centered around the sun god Aten, and also initiated some artistic changes toward realism rather than typical idealized Egyptian art. She is mostly famous because of the well-known bust of her head which is currently displayed in the Neues Museum in Berlin. Few other female figures were depicted so beautifully, and had their name known. This is why you know of her. I don't think she was particularly powerful in her own right. With her husband, many changes were made in Egypt, between the religion and switching the capital of Egypt to Tell el-Amarna, so her reign had a lot of impact, culturally. But I wouldn't really say she was unusually powerful. She is certainly the most beautifully depicted of the Ancient (Pre-Greek) Egyptian queens.

But Hatshepsut (who proclaimed herself Pharaoh and ruled in her own right, and made expeditions to Punt) and Cleopatra (who was influential and perhaps had a role in the way the Roman Empire eventually was founded, due to her relationships with the Roman ruling families) have better claims to the status as "most powerful".