Statistical approach to compare the SNP genotyping data among set of individuals So, I have the genotyping data of about 650,000 SNPs for 96 individuals. I already know the Y DNA haplogroup of these individuals, so to some extent, I have a gross understanding of their ancestry. 

What would be the best way to go about doing this? From what I have been reading, maybe a PCA would be a good idea? Suppose individuals 1-10 belong to a particular population (unique ancestary) then their SNP genotypes should be significantly similar to each other than say individuals 11-20 who belong to another population group. So, in theory I should get two clusters in my PCA plot.

I have the genotype of each SNP for each individual. How would I go about creating a PCA plot or any other alternative way of analysis for this kind of questions.
PCA sounds like a good start to see a rough population structure among your 96 individuals, this step is half a sane thing to do, but also it can give you a hint how many distinct populations there are in your dataset. I have not personally run PCA on SNP data, but it seems that there are quite lot of tutorials online. For instance this one looks  nice.

Once you know how many categories you can expect in your population, you can use Structure to classify individuals to the categories.