Hmm...I would have to go with Nefertari. I believe she was more liked, and had more of an impact on Egypt. Nefertiti on the other hand wasn't as well liked.
While I love Nefertari, in fact my daughter is named after her, she is extremely enigmatic and there's very little we know about her for certain aside from her roles as Queen and mother. For example, we no nothing for certain of her family and who her relatives were. We speculate that she wasn't a King's Daughter because she never refers to herself as such but there is also speculation that she was a relative of Ay.
Furtheremore, I don't think we can't say she had more of an impact on Egypt in fact i'd have to disagree. We know Nefertari corresponded with Pduikhipa, Queen of the Hittites, independantly of the correspondance between their husbands, but Nefertiti had a heck of a lot more power and may even have been her husband's co-regent and some speculate she even succeeded him taking the name Smenkhare.
Nefertari may have been well liked and she is very famous in her own way. Her beautiful tomb in the valley of the Queens is stunning, but it's the famous bust of Nefertiti in the Berlin Museum which is an icon of Egypt second only perhaps to Tutankhamun's mask. Her image has stood the test of time. In fact every time I tell people my daughter's name, they try and correct me and ask if I mean 'Nefertiti'. whom more people seem to have heard of.