'Oetzi the Iceman' refers to 5,300 year old mummified human remains found in the Italian Alps in 1991. A new model of Oetzi has been made for display in the museum created for him in Bolzano, Italy. Consistent with analyses of his DNA the model will depict him as having brown rather than the previously thought blue eyes. His new model coincides with the 20th anniversary of his discovery.




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how did they figure his eye color?

Genetics, eye color is a result of your DNA.


So I would presume that they have found enough DNA to find the markers that are associated with brown eyes.

Information about Otzi's DNA can be found in the paper "Complete mitochondrial genome sequence of the Tyrolean Iceman" Current Biology (2008) vol. 18, 1687-1693. (Paper by Franco Rollo et al)
There we find that Ötzi's DNA belongs to the K1 cluster of the mitochondrial haplogroup K that has not been identified in modern European populations (115 existing K lineages were compared with it).  This is the oldest complete Homo sapiens mtDNA genome generated as yet. 
Otzi died aged about 45 some 5350 to 5100 years ago. 
From Oetzi's DNA scientists had been working on what physical traits he must have had. Per the April 2010 article below:

"Now, those scientists must decipher the genetic traits – such as diseases and eye color – indicated by the order of the base pairs of Oetzi’s DNA".





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