This is a very tricky question to give a definitive answer to. There are many factors you have to consider such as blood, age and political power.
Firstly we need to look at the immortal strains.
Markus was born to the first immortal (Alexander Corvinus) and was later bitten by a bat becoming the first vampire. This meant Markus had both Vampire and Corvinus strains, this is evident in 'Evolution' because only a Corvinus strain immortal can become a hybrid. Viktor however was only a vampire strain immortal. This means he misses the added boost of the Corvinus strain which as we see in 'Evolution' gives you a very sizeable boost in all an immortal's aspects. On these grounds Markus is a clear winner as his heritage is more powerful than Viktors.
When Markus turned Viktor he had not been a vampire to long and ultimately lacked authoritative, battle and political experience that Viktor had an abundance of. Viktor had been fighting and commanding people all his life and power was nothing new to him. In a fight at this stage Viktor would most likely win because of his increased experience, we can only imagine how that fight would have gone because Markus would by no means fall easily but at the same time never he never lead a ruthless and powerful life as Viktor had. Markus may have been born into immortality and the power that came with it but Viktor mastered using power as he reigned for many years, learned how to command power and ultimately knew how to fight better than Markus. I assume this because he had a long successful reign with a powerful army to back him.
Viktor hands down. Markus had no devoted followers, armies or allies from the beginning, this is why he came to Viktor seeking assistance. He needed the few things he never had. Going through the ages as an elder he never had the presence Viktor had, this is evident in 'Evolution' when Lorenzo (Alexander Corvinus) stated that "it was never his coven". The old world coven was built with Viktors armies who were loyal to Viktor from the off. This is clear in the prologue of Evolution When the death dealers pointed their crossbows at Markus when addressed by Viktor, his soildures would have killed Markus at Viktors command. Markus always lived in Viktors shadow never standing a chance of commanding the power Viktor always did. This is shown in the known fact the Viktor stated himself as the oldest and most powerful vampire, a fact that was never disputed as Markus was always to out numbered to do anything effective about it. Markus choose for the sake of his brother and the survival of vampires it's best to knuckle under and believe in his illusion of power as an elder.
I could go on but the evidence is insurmountable. Viktor ruled!
Power (raw power)
When we ask the question of who is better? We really mean. In a fair fight without weapons who would reign victorious? We imagine both of them squaring off against each other like Michael and Viktor only without the sword.
This is a tough one because Markus changed into a hybrid after Viktor died becoming near unstoppable. Under these circumstances Markus would clearly win. It took Selene the boosted power of Alexander Corvinas's blood to give herself a fighting chance.
If you consider them fighting in the early days when William was free, Viktor would have most likely won through skill and experience. Markus had a strength advantage due to his heritage. This sadly does not mean a great deal at the time due to the lack of experience for markus and power for Viktor.
Michael had a strength advantage over Viktor when they fought which was clear as he brought Viktor to his knees giving him a fight he has most probably not had since Lucian.
However Viktors 14+ centuries experience with combat and using his immortal skills saw him overcome raw strength as he knew how to take the high ground and over power Michael. Michael was running on pure strength as he had no battle experience and had been an immortal for about 30 seconds.
This example shows how pure strength does not always wins battle, your wits and developed skill give you an upper hand. Having said that you have to consider that Markus lived a completely immortal life in full control and knowledge of his powers, he lacked the experience in combat and battle skill Viktor had which would indeed tip the scale. In these circumstances the result would realistically be the same as Viktors altercation with Michael, cutting the final result pretty close but surely enough siding with Viktor as his advanced knowledge of combat and battle skill combined with his new found power would have made him a deadly adversary and the ultimate winner.
Fastforward 14 centuries to Markus's rightful time to rule in 'Underworld', I think thing would have been fairly level but tipped in Markus's favour. At this point in time they are both very old having came to power to close in time to make any long term significant difference. Both have experience in combat, killing and exercising their immortal skills having both fought against lycans and ruled throughout the centuries. In the Underworld franchise one clear fact we learn is age = power. Having already show Markus would have the power advantage but lack of experience to Viktor, in 'Underworld' this would not be the case. Both vampires would have 14+ centries combat experienced to the point Viktors human years would now give him no advantage which brings things down a bit for Viktor. Markus would have a power advantage but unlike before he would have the experience to compliment his power. This would make him more of a threat to Viktor as he cannot take advantage of Markus's lack of experience. Through sheer power of strains Markus would have an upper hand. Ultimately Markus would win, their experience and skill being level it would come down to who has more power which is Markus. The only way Viktor would stand a chance of a clear win is if he had the other two immortal strains, other than that it would be a well fought fight but with Markus logically topping out. This does not mean Viktor would go down quietly, he was a powerful vampire who would have put up a fight deserving of the title 'Elder'.
This is my opinion based on my extensive knowledge of the films, lore, strains and characters. I made my decision on the logicality of the franchise and the expressions of power I have seen in the films and how each character tops out over the other.