Cook the edamame in a large pot of boiling water until crisp-tender, about 3 minutes. Drain. Rinse with cold water, then drain well and pat dry. Repeat with the green beans and yellow beans. Combine the vegetables in a bowl.
Add the vinegar, oil, herbs, 1 teaspoon of salt, and 3/4 teaspoon pepper to a glass screw-top jar. Seal the jar and shake vigorously to mix the vinaigrette.
When you're ready to serve, shake the jar again to re-mix the vinaigrette and pour it over the vegetables. Season with more salt and pepper, if desired.
Alternate Method: Whisk the vinegar, 1 teaspoon of salt, and 3/4 teaspoon of pepper in a large bowl to blend. Gradually whisk in the oil. Add all of the beans, tomatoes, basil, and thyme, and toss to coat. Season the salad, to taste, with more salt and pepper, and serve.