The Wikipedia article picks one of many pieces of research to quote. Your criticism are fair as a criticism of that specific research paper. But after you've looked at a dozen of them, continuing to say that it is just an artifact of terrible methodology (even though most actually are terrible) becomes much harder to support.
But that said, here is a classic test showing strong gender differences accidentally discovered by Piaget. Draw two cups, one tilted. Assuming that both are halfway full of water, ask the subject to draw the water line.
Until puberty, neither gender can perform this task well. After puberty around 90% of men and 30% of women find it trivial, while the rest do not. (The most common answer that I have seen from women is to tilt the water line with the cup. The second is to tilt it double!) Performance on this task is not particularly correlated with education.
Ask a few friends and family, and it isn't hard to verify for yourself that a gender gap exists.
Interestingly I have yet to encounter a programmer, male or female, that doesn't find it trivial. I have no idea why programming would select for people who find this task easy. but it apparently does. And the population of people who find this task straightforward has 3x as many men in it as women.