The comparison with Sampras is quite interesting and makes more sense than one might gather at first glance. (I explored this very topic in a group chat back in June, in a reply to
@Bender much of which follows with added stats and minor editing.) Of course the stock retort is that at least Rafa reached two finals at the YEC while Pete couldn't even manage a single one at RG, but there are only 5 rounds in the former while a major requires 7 hurdles to clear. That's one caveat that has special bearing here as it's generally agreed that burnout was the big reason for Pistol's straight-set loss to his career pigeon Kafelnikov in the SF (more on this shortly) - not to mention that you can take one loss and still win the YEC (in fact Pete never won the whole shebang undefeated, three times thanks to Becker who may well be the best indoor player ever), but since Rafa didn't suffer a RR loss in the two years he reached the final we'll ignore this part - but the follow-up will be that YECs tend to attract superior opposition so let's look at each guy's actual draws.
Pete at '96 FO:
SF - Kafelnikov
QF - Courier
4R - Draper
3R - Martin
2R - Bruguera
1R - Gustafsson
Rafa at '10 YEC:
F - Federer
SF - Murray
RR - Djokovic, Berdych, Roddick
'13 YEC:
F - Djokovic
SF - Federer
RR - Ferrer, Berdych, Wawrinka
On paper Rafa's opposition does look somewhat more impressive, but when you dig deeper he's really got only one big win in the '13 SF vs. Fed. Two if you include the '10 RRer vs. Novak, which still is the same # of Pete's own big Ws at '96 RG against almost-turning-back-the-block Bruguera and Courier. (I'd say '96 Martin and '10 Murray more or less cancel each other out.) And while Kafelnikov in '96 won "only" 57.6% of his games on clay (excluding TBs) his conversion rate at RG was a stellar 64.3% (all FO stats in this post include TBs) - higher than Fed's 58.4% in '09 and just barely below Novak's 64.9% in '16 or Muster's 64.5% in his celebrated '95 season where he won 62.0% overall. There's no guarantee that even in-shape Pistol gets past this Kafelnikov at RG or, for that matter, Rafa vs. a comparable opponent at the YEC.
Plus Pete's '96 FO run isn't his only notable one on clay, in fact I personally like to nominate his '95 DC heroics as the single greatest achievement of his career. Let's look at his DC opponents on clay that year:
QF - Furlan, Gaudenzi
F - Chesnokov, doubles w/Martin vs. Kafelnikov/Olhovskiy, Kafelnikov again
We can dismiss the QF and you could add Chesnokov was past his prime by then, but Pete's victory over the
scrappy Muscovite (who, like all good
comrades, treated DC very seriously) was a hard-fought one, and when you couple that with his unexpected next-day doubles duty and the following day's masterclass against next year's FO champ (who FYI won a respectable 55.7% on clay in '95 which probably was higher as he played 6 of his 8 singles DC rubbers on the surface) you can easily argue that his performance in the '95 DC finals was as good as anything from Rafa in any indoor setting, if not even better.
Now one could counter that if we're counting Sampras' DC performance Nadal's
five DC title runs must also be considered, but Rafa's major DC triumphs have come mostly on clay and when we compare players' indoor records we're almost invariably talking about their performance on hard/carpet. What else then? Rafa's '05 Paris is more or less equal to Pete's '94 Rome, while the former's '13 Brasil Open on clay is about as meaningful as the latter's '92 Kitzbühel or '98 Atlanta. Maybe you feel differently but I'm not seeing much of a gap between the two.
One thing I'll grant Nadal is his superior longevity/consistency, though even here I could argue that Pete's comparable resume in a shorter time frame is in fact a point in his favor. But the purpose of this analysis is not to argue Pistol was a better clay-courter than Rafa the indoor player, but to point out that these two were similarly strong (or not) in their prime and merely glancing at each's best FO/YEC records is a poor way of judging their actual respective prowess on clay/indoors. Both could play inspired tennis anywhere, but would fall short of other GOATs on their own weakest surface more often than not.
