That's a very good question, Su.Ki. My wife who "discovered" the stuff (which is being heavily promoted in the U.S.) thinks it is pronounced "Keen-wa." However, a Mexican language partner did not recognize it when I pronounced it that way, and asked if I mean "Keen-oh-a." However that was a side issue and I didn't stop to be sure--it was actually a discussion of whether I was preparing a hot drink called atole, made with oatmeal and amaranth, correctly.
Ahdictionary.org is showing both options: (kĭ-nōə, kēnwä).
Where is the stuff from? Click: "Andean region of Peru, Bolivia, Ecuador and Colombia", https://en.wikipedia.org/wiki/Quinoa , and it's Quechua word. So perhaps people in Mexico, who are tuned into Nahuatl but not Quechua, use a "hispanicized" pronunciation or something.