If the two spared as Jedi, Dooku would probably win the match because he was the better all-around duelist. But if this issue's fight had continued with Windu as a Sith, Windu would have been able to turn the tables.
Count Dooku didn't like the Jedi Order, but he particularly disliked Master Windu. Disney+'s Star Wars: Tales of the Jedi explains why.
Dooku could have not beaten Yoda in Geonosis, meaning that the fight would have ended with Dooku either killed or captured had it continued. At that point, the only two Force-sensitive warriors who could beat Yoda in a fight were Mace Windu and Darth Sidious.
Both are known to be among the greatest duelists in Star Wars lore. Dooku took on Anakin and Obi-Wan simultaneously on two occasions, and managed to incapacitate one of them both times. Windu comprehensively defeated Sidious in 1v1 lightsaber combat, when even Yoda couldn't achieve that.
Before Dooku was a Sith, he was an esteemed Jedi Council member. As Windu's senior by 30 years, he saw Mace grow up and mature in the Jedi Order. That's why he referred to Windu as an “old friend” in this comic.
This isn't to say that Mace Windu isn't powerful when it comes to the force. He's on par with Darth Maul and is more powerful than Qui-Gon Jinn. But, Obi-Wan is still the stronger Force user which makes him a powerful combatant.
Abilities. Lightsaber Combatant: Dooku was extremely skilled in lightsaber combat, and a gifted duelist. He was one of the few known individuals who could fight Yoda as an equal.
It's not even up for debate that Darth Vader is stronger than Count Dooku. Even before he was at full power, Anakin Skywalker was able to overpower Dooku simply based on his lightsaber training. Had Dooku fought Darth Vader at full power, the fight likely would have been a lot shorter.
With Dooku dead and very likely Windu dead, much of the same would have occurred. The Jedi would still be outnumbered by battle droids and would have to fight at a disadvantage until Yoda arrived. Jango Fett would face the Jedi and at some point find himself facing Kenobi or Skywalker.
Anakin regrets this decision, and Palpatine reasons with him saying that Dooku was too dangerous.
In one of the canon comics Sidious outright implied that Maul was pretty much head and shoulders above Dooku when adressing the potential. While Dooku was a useful pawn for him, Maul in the other hand seems to be actually his first choice as a heir before Anakin was really part of the picture at least.
Yes, Sidious did let Windu beat him
There were two ways in which Sidious was nudging Anakin towards the Dark Side throughout Revenge of the Sith: Promising Anakin that through the Dark Side, he could save Padmé from dying during childbirth.
Although Dooku hopes this will allow him to rule the galaxy alongside Sidious, whom he secretly plots to overthrow, he is ultimately betrayed by his master, who arranges his death at the hands of his eventual replacement, Anakin Skywalker, who later falls to the dark side and becomes Darth Vader.
Darth Vader. Mace Windu can obviously put up a somewhat decent struggle, but he can't win, nor is he Vader's equal. Basically, Mace Windu might have two advantages against Vader, his Vaapad and his shatterpoints awareness, not only against Vader, but against most darksiders in general.
Bottom line, Dooku never considered himself a Sith. And he wasn't; he was a man looking to change the galaxy in a way the Jedi were unwilling to try. And that is why he joined the Sith and became Darth Sidious' apprentice, Darth Tyrannus. When Dooku became Sidious's apprentice, he was already an elderly man.
As powerful as Darth Sidious may have been, it's easy to forget he actually seemed afraid of Master Yoda. As seen in Revenge of the Sith, Palpatine initially thought he could deal with the aged Jedi Master - and then, when Yoda proved able to counter the Sith Lord's Force lightning, he fled.
Dooku belonged to the aristocracy, and his weapon reflected an older, more chivalric style than the Jedi he faced. It also reflected his status as the head of the Separatists: the lightsaber looked far more ceremonial than practical, suggesting that he himself did not face combat nearly as much as the Jedi did.
Count Dooku would destroy Kylo Ren incredibly quickly. In terms of physical abilities Dooku may lack extreme stamina due to his old age. However this hasn't prevented him from facing off against the combination of Anakin and Obi Wan multiple times.
In a private hangar, as he made his escape from Geonosis, Dooku was confronted by the Jedi Knight Obi-Wan Kenobi and his Padawan, Anakin Skywalker. Dooku was easily able to best his opponents with his lightsaber, wounding both Kenobi and Skywalker, the latter of which Dooku severed his arm after a brief duel.
More sophisticated, more calculating, and if anything deadlier than Maul, Count Dooku proved himself more than a match for the combined skills of Obi-Wan Kenobi and Anakin Skywalker in Attack of the Clones.
Master Yoda has risen above all others to claim the top spot as the most powerful Jedi of all time and the true chosen one according to IGN's audience. He won pretty handily as well, as he was victorious in 89,756 of his 95,243 battles and had a win percentage of 94.2%.
It's already well-established that Qui-Gon was incredibly strong with the Force. He continuously studied the ways of the Force and eventually learned enough about the Cosmic Force and the Living Force to unlock the secrets of eternal life.
One of the main reasons why Yoda would've won against Anakin is simply because he was far better trained than him. Yoda could see the moves his opponents were going to make before they made them; therefore, battling against Anakin would've put him at a far heavier advantage.