Press the extra firm tofu for 15 minutes to remove excess moisture, then cut into 1-inch cubes.
In a small bowl, whisk together the tamari, rice vinegar, minced ginger, minced garlic, red pepper flakes, and water to create the stir-fry sauce.
Heat the sesame oil in a large skillet or wok over medium-high heat until shimmering.
Add the tofu cubes to the skillet and sear until golden brown and crispy on all sides, approximately 8-10 minutes.
Add the broccoli florets, sliced red bell pepper, and snap peas to the skillet with the tofu.
Stir-fry the vegetables for 4-5 minutes until they are tender-crisp and maintain their bright color.
Pour the prepared ginger-garlic sauce over the tofu and vegetables, then add the shelled edamame.
Toss everything together for 2 minutes until the sauce thickens slightly and coats all ingredients evenly.
Season with sea salt and black pepper to taste before serving immediately.