Hard to tell, first of all this is all only IF. Right now it is all hypothetically. Right now it seems like Pete has clearly the edge - 14 slams over 10, more weeks at No.1, years ending No.1, most Wimbledons as most valuable slam, but maybe in 2-3 years it could be closer between them. Actually right now only thing Rafa has the edge is clearly career slam and also RAfa´s best season is better than Pete´s best season. Someone can argue that Rafa´s career slam is not worthy so much, because of homogenization of surfaces, but one thing must be said - Rafa won all 4 and Pete didn´t even came close to it, and i am sure he wouldn´t win RG in any era, simply his tennis wasn´t suited to clay courts and his movement was horrible on clay, despite the fact that he was great athlete and had great footwork. Maybe problem was also his motivation, he maybe didn´ thought he can win there, RG didn´t mean much for him, maybe if he was trying harder he could at least make F there- but still don´t think could won- most likely would los in F to some hot clay-courter, but career slam didn´t mean that much in 90s because since Laver nobody did it so Sampras maybe didn´t even thought about winning RG as really important thing, something like Roger- badly want to do, because it was last slam he was lacking, Pete never felt that way for sure. About Rafa - he did won all slams and we can admit that he show he can win on today´s grasss- great footwork for grass, and is arguably 2nd best grass player in last decade, won both HC slams only once but show that his A game on HC is pretty good for slam title for sure, so his career slam i think is worthed to mention that he did it on 3 surfaces, while Pete always was good only on 2 that is huge difference in term of overall achievements i think, but Pete is clearly ahead of Rafa in every other statistics, but the truth is Rafa was ,,forever,, 2nd, while Pete didn´t have nobody as good and consistent than Roger - i mean Pete never was good on clay and still was 1st all the time, imagine somebody really good on all surfaces or healthy Agassi -motivated all the time, how badly PEte´s No.1 position could be. So i think Pete is at this moment better in history and even if both will be 14-14 most likely Pete will be ahead, because i don´t believe Rafa can surpass No.1years and No.1 weeks, but we will see in future. But generally they played in different eras, different conditions, hard to compare really - just for imaginations give Nadal in 90s and Pete in today´s ATP tour, how many slams will they achieve? nobody know, because Pete won´t be playing SV so often and Rafa won´t be so succesfull with topspin, because he woulnd´be able to generate so much topspin on his shots, so basically both are products of their eras, we can say Rafa would achieve much less in 90s and Pete much less in today´s tour, because everything is slower, baseline tennis rules, but still it is only guessing.
. Unfortunately, now it will hurt your mind. 
