Thor is a genuine god with planet-level power; Homelander is a powerful mortal who cannot compete at that tier.
Thor has fought the Hulk to a standstill, wielded divine lightning that cracks planets, and survived encounters with cosmic entities. Homelander's best feats are building-level strength and tanking military weapons. The power gap is enormous.
Homelander's heat vision is his strongest attack, but Thor has survived attacks from beings like the Celestials and Galactus. His Asgardian physiology provides resistance to energy attacks far beyond anything Homelander can produce. Meanwhile, a single swing of Mjolnir would generate more force than anything Homelander has experienced.
Homelander's fragile ego would crumble the moment he realizes nothing he does hurts Thor. The God of Thunder has faced truly terrifying cosmic threats and never wavered. Homelander has never faced a genuinely superior opponent and lacks the mental fortitude to handle the realization.
Homelander has flight, heat vision, and has never been truly defeated in direct combat. His full power ceiling is untested, leaving uncertainty about his maximum output.
Thor wields Mjolnir, commands planet-cracking lightning, and has strength rivaling the Hulk's. He has fought cosmic entities and his Asgardian physiology makes him virtually invulnerable to Homelander's attacks.
Thor wins overwhelmingly. Homelander is a powerful mortal; Thor is a god who fights alongside and against cosmic entities. The tier gap is simply too vast.
Homelander also fights
Thor (Norse) also fights