Najaf is also known as Najafe Ashraf ie the The Most Noble city of Najaf.
After the Holy Prophet a.s , Imam Ali being the most Noble and excellent of Mankind resided in this Holy city. He practised all the teachings of Allah and the last prophet s.a.w. so wherever he laid his footsteps upon of course becomes the most Noble too.
As for Kaaba known to be Shareef ie Noble, it is a title that is not mentioned anywhere in the Holy Quran where we have Baytul Mamoor, Baytul ateeq, and so forth. Comparing both Kaaba and Najaf being Noble and Most Noble is not the right thing because each one carry a special status although it is the presence of.the most Noble of.mankind that we will.come to.know about the significance of the Kaaba and Allah Himself has approved of this in so.many.verses of the Noble Quran!