It's no secret that Thanos and Invincible's Omni-Man are among the most powerful beings in their respective universes, but who would win in a fight?
To really settle this debate, Thanos without any gems will be considered as Omni-Man could just as easily put on the gauntlet. Thanos's superhuman abilities derive primarily from his parentage by two Eternals. His powers are enhanced by a Deviant mutation, bionic amplification, and upgrades from Death herself. He has a large array of superhuman abilities. He is essentially immortal as he cannot die of old age, is nearly invulnerable, and has returned from death multiple times. His incredible strength, speed, agility, and fighting skill allow Thanos to physically outclass other powerhouses like the Hulk. In combat, he has also displayed the ability to blast cosmic energy. Somehow even more essential to The Mad Titan's cosmic presence is his intelligence, ambition for power, and indomitable will.
On the other hand, Omni-Man is the Invincible universe's distorted Superman analog. He is of a species of superpowered beings who live thousands of years called Viltrumites and is among their most powerful. Like Superman, he can fly, has super strength, and super speed. He is nearly invulnerable to physical damage and heals extremely quickly. He was able to single-handedly kill the Guardians of the Globe, the Invincible universe's Justice League pastiche. He is ruthless and skilled, having killed many super-powered beings over thousands of years. If the two powerhouses were to fight, the resulting battle would be brutal and devastating. They are both cosmic-level entities, capable of single-handedly conquering planets and toppling armies. Neither combatant has any true stated weakness. Both are nearly immortal, immensely powerful, and relentless in battle. In the end, though, only one can remain standing. Thanos, the Mad Titan, would claim victory due solely to his more varied powerset.
Although Omni-Man is immensely powerful, his only tactic in battle is brute melee force. He flies at incredible speeds and uses his physical strength to tear apart his enemies. In Invincible, we see time and time again that Omni-Man's only strategy in a fight is to physically overpower his target. Thanos's strength and speed are comparable but likely lesser than that of Omni-Man. However, throughout the history of Marvel Comics, we see he has a much more versatile toolset.
Thanos's sheer intellect makes him a master tactician and allows him to create and use technological marvels of his own design. Due to his Eternal heritage, Thanos can manipulate matter on an atomic level. His explosive beams of cosmic energy allow him to perform devastating ranged attacks. He has been shown to be able to get into enemies' minds using telepathy. He has used telekinesis in battle. He has even demonstrated advanced knowledge of the mystic arts. Despite being one of the most powerful characters in comics, Omni-Man would not be able to survive against Thanos's diverse and incredible repertoire. Thanos wins.