Superman would easily win against Homelander. Superman has proven to be one of the most powerful beings in DC comics. He was noted as being “The most powerful man alive.” In Action Comics No. 924, he is described by a Marine General as a “living Nuclear Weapon”, when Superman leads an invasion of Russia to take down General Zod. His abilities include flight, heat vision, super strength and invulnerability – which makes him unparalled with his versatility and skill level high enough to conquer any adversary, even Apocalypse or Thanos at peak condition for short periods of time without tiring out like lesser characters such as Spider-Man would if they tried beat these foes too quickly. He is said to be so strong, that not even a nuclear bomb could kill him. Superman can move planets and has been stated to be capable of moving solar systems over his abilities.
In addition to his powers, Superman’s physiology is also highly durable and resistant to many forms of damage including bullets, arrows, fire, ice, acids, etc. It is also stated that Superman does not need to breath or sleep. He can survive in the vacuum of space and his lungs have the ability to hold his breath for 20 years before having any adverse effects. His powers are so vast that he even has the power to time travel as seen in Kingdom Come when he travels back 18 hours into the past.
On top of all this, Superman’s speed and agility are high enough where he can move at hypersonic speeds (capable of moving half a mile in less than 2 seconds) and dodge almost every attack thrown at him by kryptonians like Zod who himself said Superman was “faster than lightening.” He is also resistant to telepathy as proven when Superman as Clark Kent was capable of resisting a telepathic attack from Martian Manhunter who has mind reading abilities capable of probing the minds of even those who have mental blocks, such as Batman.
In contrast, Homelander is nowhere near being on Superman’s level. In fact, he isn’t even a real Captain Marvel villain – just a no name knock off with a scarlet cloak and belt that bombards you with God awful puns. This guy wouldn’t be able to scratch someone like Doomsday let alone Superman himself. His durability is also downplayed at best; for example in The Boys #19 he gets his neck snapped by Vas (one of the gangsters working for Payback). He later recuperates in The Boys #20 (it takes 3 issues to heal a broken neck when you’re bullet proof), but still, it proves how easily he can be hurt. He also references that he doesn’t feel pain in his heart when Butcher shot him there in issue 37; however, it is stated that the only way you can kill Homelander (besides decapitation) is by shooting him in the head – which means even with his durability downplayed it would still be hard for Supermaan to pierce through Superman’s skin unless he uses heat vision.
Finally, a durable man like Homelander isn’t going to be much against someone who has invulnerability and super strength like Superman.