Like any two generals (or any two people in any profession), Grant and Lee each had their own strengths and weaknesses. It is possible to identify these strengths and weaknesses relatively objectively, but it is not possible to objectively say which was the better general.
Basically, their strengths and weaknesses were exact mirror images. Lee was a great tactician. He was really excellent and knowing how to win battles in creative ways. He understood the abilities of his commanders and how to use them. He was generally able to win battles even against superior forces. By contrast, Grant was not a great tactician. He seemed to only know how to win battles by having more troops and by having them conduct frontal assaults on the positions they wanted.
On the other hand, Grant was excellent at strategy. He had a much clearer idea of how to win an entire war than Lee did. Lee, it can be argued, was too aggressive in attacking the Union army when his own army lacked men and would have been better off in the long run being more defensive. By contrast, Grant clearly understood that the North had more men and supplies and that winning the war involved things like keeping constant pressure on the Confederates so as to gradually wear them down.
Thus, Lee was better at fighting individual battles, but Grant was better at overall strategy. Both were great generals in their own ways.