We prefer the cooking method below which is recommended by Martha Rose Shulman. Ms. Shulman's recipes appear weekly in The New York Times.
Since cooked quinoa freezes perfectly, cooking a larger than needed batch provides pre-cooked quinoa for a very quick meal to be made at a later date. We do the same with wheat berries since the cooking time for that grain is lengthy.
Place the quinoa in a large bowl and cover completely with cold water. Let sit for five minutes and drain through a strainer, rinsing until the water runs clear. Bring the 3 cups of water to a boil in a medium saucepan. Once boiling, add the quinoa; bring back to a boil, and reduce heat to low. Cover and simmer 15 minutes or until the quinoa is tender and translucent; each grain should have a little thread. Drain the cooked quinoa in a strainer and return quinoa to the pan. Cover the pan with a layer of paper towels or a dishtowel, replace the lid and allow quinoa to sit for 10 minutes. At this point, the quinoa can be used for your recipe, or cooled and placed into plastic bags. Flatten the bags, seal and freeze.