In a 5- to 6-quart pan over high heat, bring about 3 quarts water to a boil. Add noodles and cook until tender to bite, 3 to 6 minutes. Drain noodles and rinse gently under cold running water until cool.
Meanwhile, in a large bowl, mix rice vinegar, soy sauce, sesame oil, and wasabi. Pour about half the dressing into a small bowl and reserve. Add noodles to the large bowl; mix to coat. Cover and chill until cold, about 1 hour, or up to 4 hours.
Just before serving, add reserved dressing to noodles and mix to coat. Sprinkle salad with green onions and bonito flakes, if using.