Prepare the tofu: Drain the extra firm tofu and wrap it in a clean kitchen towel. Place a heavy skillet on top for 15 minutes to press out excess moisture, then cut into 1-inch cubes.
Make the stir-fry sauce: In a small glass bowl, whisk together the tamari, rice vinegar, minced fresh ginger, minced garlic, red pepper flakes, and water until well combined.
Sear the tofu: Heat the toasted sesame oil in a large non-stick skillet or wok over medium-high heat. Add the tofu cubes in a single layer and sear for 8-10 minutes, turning occasionally, until all sides are golden brown and crispy.
Sauté the vegetables: Add the broccoli florets, sliced red bell pepper, and shelled edamame to the skillet with the tofu. Season with sea salt and black pepper. Stir-fry for 4-5 minutes until the vegetables are tender-crisp and vibrant.
Finish and glaze: Pour the prepared ginger-garlic sauce over the tofu and vegetables. Toss continuously for 1-2 minutes until the sauce thickens slightly and coats every ingredient beautifully.
Serve: Transfer the stir-fry to a bowl and enjoy immediately while hot and fragrant.