You are wrong. Completely wrong.
Why do you assume that the indigenous people of an entire continent would all look the same? Do all Europeans look the same? Of course not.....and they are majority Caucasoid.....and from a much, much, much smaller land mass. Puerto Rico is quite close to the equator......it would be silly to think indigenous from there, would look the same as indigenous from the Washington area. Or New York.
Regardless, many Puerto Ricans have ancestry from a variety of social race groups. African, Cacasiod and Americanoid. Some are a mix off all three. Some a mix of just two. Some only from one. Puerto Rican is a Nationality.....in these modern times, with immigration, they can be from any part of the world.
I am sure there are more than a few Puerto Ricans that do have blue eyes. Have you met every, single one of them?