Pack the onions into a 1-pint mason jar or similar heat-safe vessel. Place the jar in the sink to catch any splashes of hot vinegar.
In a small saucepan combine the water, both vinegars, maple syrup, salt, and pepper flakes. Bring the mixture to a gentle simmer over medium heat, then carefully pour the mixture into the jar over the onions.
Use a butter knife or spoon to press the onions down into the vinegar and pop any air bubbles in the jar. Let the pickled onions cool to room temperature, at which point they should be sufficiently pickled for serving.
Cover and refrigerate leftover pickled onions for later.