In a small saucepan over medium heat, combine clams and their juice, and extra clam juice. Bring to a boil, then remove from heat and set aside.
In a large saucepan over medium heat, melt butter. Cook onions and thyme in butter until onions are soft. Whisk in flour all at once to form a paste, cook 1 to 2 minutes more. Whisk in clam mixture. Stir in potatoes, reduce heat and simmer 15 to 20 minutes, until potatoes are tender. (At this point the soup can be cooled and stored for later use, if desired.)
Puree tofu in a blender or food processor until smooth. Stir into soup and heat through. Season with salt and pepper.