All 3 of them would bother him in some different ways on different surfaces, conditions.
Rafa would probably defeat him at RG because he's the God of Clay, but I think that he would struggle a bit on other surfaces(hard, grass) against Alcaraz. I don't see Alcaraz having too much issues with Rafa's lefty cross court heavy topspin forehand outside of clay(where the bounce would be lower). Alcaraz can also actually match peak Rafa in athleticism(speed) and strength(power). I feel like Rafa would dislike playing Alcaraz the most out of the big 3(at least outside of clay). I don't particularly like Nadal's deep court position against Alcaraz - I think Carlos would fancy that.
I think peak Fed would school Alcaraz on grass because there's a huge difference here in spot serving(maybe the best spot server ever vs a mediocre one). Roger also takes time away beautifully(best transition game ever, probably) and Alcaraz is bothered if he's rushed and not in control(dictating) of the points. Situation would probably be similar on hard court(particularly faster ones). Carlos also doesn't have the craftiness, racquet talent advantage against Roger that he does against most of today's opponents. But, I could see Roger struggling against Alcaraz on clay, where serving doesn't matter as much and he wouldn't be able to rush Alcaraz easily. Roger would probably get overwhelmed there by Alcaraz's power(pace generating) advantage and defensive abilities(speed).
I think peak Novak definitely beats Carlos on hard court. He's the best pace absorber and redirector in the history of the game and Novak's machine like consistency and depth would suffocate Alcaraz and really frustrate him. Novak probably beats him on grass, as well, but it would be closer. Alcaraz overwhelmes opponents with pace and Novak's pace absorption and redirection, ability to protect the backhand side like no other plus Novak's relatively close court position and speed would really bother Alcaraz(taking away the drop shot, for the most part). We have seen that Alcaraz doesn't enjoy playing Sinner, and Novak resembles Sinner the most out of the big 3. Not as much pure baseline power, but more consistency, precision, depth, mental strength, better volleying...
On clay, I would say it's a 50-50 match, maybe slight advantage to Carlos. I could see Carlos just overpowering, overwhelming Novak in Nadal, Wawrinka, Thiem style while Novak would struggle to finish points on slower clay.. But I could also see Novak frustrating Alcaraz with his usual package(consistency, depth, pace absorpbion and redirection, taking away the drop shot for the most part, counterpunching, possibly outclutching Carlos in the tight moments...).
When I take into account all surfaces, I think Alcaraz would generally struggle the most against Novak, and then probably Fed on faster surfaces(particularly grass and most hard courts in general). Carlos probably beats Nadal on hard and grass, loses on clay against the King of the surface(obviously).