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A brief comment, the word "gender" is used to refer to the self-identification of a person whereas "sex" is the biological sex at birth.
https://en.wikipedia.org/wiki/Sex_and_gender_distinction
NGS data cannot give you a person's gender, you just need to ask them :-)
Thanks. I do think that you can extract sex from a chip call. for many sites (which are gender-specific), males would have just one allele, and the other one is missing (loci on X chr.). females would return null result for Y loci
I am a bit unfamiliar with SNP based identification but didn't people use certain paralogous markers for that: http://www.ncbi.nlm.nih.gov/pubmed/20235797
So you already know the answer, you just have to look at markers on the X (excluding the region which pairs with the Y) and compare heterozygosity, males are hemizygous so would appear "homozygous" for all those loci. I have no idea if SNP chips have markers for the Y, but if they do, yes, you should use this information as well.
edit: Sorry, my post is not a reply to Gabriel R. comment but instead to erezts just above.