My answer would be that there is no canon answer for this without extreme digging and extrapolation.
My reasons being:
Nothing can be found on the wikia, Pottermore or from the books or from a interview(to my knowledge) that talks about a certain percentage.
Someone could however name all of the Half-muggles into a grouping and name which parent was a muggle and make a percentage from that. But that is all I know that would work.
My list(if I am wrong feel free to edit or downvote):
Gilderoy Lockhart- father
Minerva McGonagall- father
Malcolm McGonagall- father
Robert McGonagall Jr. — father
Tom Marvolo Riddle/Lord Voldemort — father
Severus Snape — father
Bowman Wright — father
Mafalda Hopkins- mother
Dean Thomas — mother
So saying this is all true, then the percentage of muggle fathers is larger than muggle mothers. Also, I consulted the canon where I could, but most of this is taken from the wikia, so reader beware.
2/11 muggle mothers
9/11 muggle fathers
And from that data you could make a percentage from that.
But if this is your answer I fail to see what it proves, sorry not a diss.
Primarily the wikia.
I used the wikia page above to compile this information. And since some of the info I did not know was right or wrong I added another list that I sure of is right and from the book. Some of the information might be from Pottermore that was on the wikia, but I cannot confirm this.
My edited list:
Seamus Finnigan- father
Tom Marvollo Riddle- father
Severus Snape- father
Dean Thomas- mother(He states in the Deathly Hallows that his father left when was little so he didn't know if he was a wizard or not. This makes it possible that he could be a muggle-born or Half-muggle)
From this though we can see that the father ratio is still higher than the mother, because there were basically no Muggle woman that had children with wizards.
Unless, you name the woman that was supposedly killed in Deathly Hallows after she said that she did know where someone was(I forget the details). But there is no proof that she was muggle or a squib. But the ratio would still be favoring fathers.