Sampras (and Agassi for that matter) do suffer in these kind of comparison because even in the 90s AO wasn't really on equal terms with other slams (Agassi didn't even play it until 1995 and Sampras skipped it in 1999 to play golf) and of course there's the 16 seed system which allows for more upsets (in general 90s had more of these "big hitter blows you off court" type upsets). However that just doesn't hold water today when AO is clearly a legit slam, able to stand on its own, you have to take the current era into consideration as well if you're making a comparison.
Also keeping in mind that Novak regularly goes deep in nearly every big CC tourney in the season (unlike Sampras and even Agassi barely has had any prep for FO) which means his season is generally busier. One of the reasons I feel he's often so beat up and listless when USO rolls around. Novak is just not that good at scheduling around and peaking for slams, picking his battles.
Personally, while his consistency on HC is very impressive, the main reason I put Novak above Sampras and about on par with Fed is some of his peak runs at AO which were downright scary in terms of level of play. Especially 2008 AO comes to mind as a complete performance balanced between great defense, offense and serving (where that 2008 serve went will always be a mistery to me when it comes to Novak, it only somewhat re-appeared 7 years later in 2015) though his 2011 and even 2016 (aside from that weird match with Simon) are amazing as well.