Funny, the 18th dynasty is my passion and I can only recall one black image of a queen and that's the infamous Yew head of Tiye, which, as has been pointed out, would have originally been yellowish.
The first Pharaoh of the 12th dynasty was described as being the son of a woman of 'ta set' (sic) meaning a nubian woman. The queens of the 12th dynasty were without exception sisters or occasionally daughters of their husbands so presumably the 'black' genes were preserved.
The 18th Dynasty was local to Thebes in origin. Queens Ahhotep, Ahmose Nefertari and Ahmose Merytaten were all apparently sisters of their husbands, and hence 'local girls'. Mutnofret, wife of Thutmose I and mother of his sons may or may not have been identical with the King's Daughter Mutnofret memorialized in a contemporary inscription and so a sister or daughter of Amenhotep I. Ahmose, the mother of Hatshepsut, is described as the sister of her husband which may mean she belonged to his family but not the Ahmossid line.
Thutmose II married his half sister the famous Hatshepsut. His son was born to a lady of the Harem of unknown origins who was later raised to the rank of Great King's Wife and Mother of the King by her son Thutmose III.
He in turn had several Great Wives, none of whom appear to have been non-Egyptian, nor portrayed as black skinned. The mother of his heir was Merytre Hatshepsut who was the daughter of a Priestess of Amun and so a local girl.
Amenhotep III had several ladies in his harem but which was his great wife is unknown. The mother of his heir was Mutemwiya, a lady sometimes identified as a Syrian princess or as a sister of Yuya, father of Tiye, but never as a Nubian.
Tiye's non-nubian origins have been covered above. Nefertiti has been identified as a daughter of Aye, (and Yuya's granddaughter) or sometimes a Mittanian princess. She too was not a Nubian, though she did wear a 'nubian' style wig.
So exactly who were these Nubian queens.