My personal opinion? To put a modern ethnic concept to what they were would be, native egyptian with the eventual mix of surrounding cultures. Sorry, but I just can't get into the afrocentric ideas about Egypt. It's very clear that they saw themselves different culturally and phenotypically for the most part from their neighbors in the north and south.
Lol but there's an array of different features all throughout modern Egypt, with the southerners having more African dna than the northerners, so saying "native Egyptian" is pretty vague.
And the Nile was not always populated, so where do you think the first inhabitants migrated from ?