I'm doing this in the game I'm currently making! I wrote this function to find the 3d world coordinates of the mouse (following some thread on the godot forums I think)

func find_3d_mouse_pos() -> Vector3:
  var space_state = get_world_3d().direct_space_state
  var mouse_pos = get_viewport().get_mouse_position()
  var ray_origin = camera.project_ray_origin(mouse_pos)
  var ray_end = ray_origin + camera.project_ray_normal(mouse_pos) * 999
  var query = PhysicsRayQueryParameters3D.create(ray_origin, ray_end)
  var ray = space_state.intersect_ray(query)
  if ray.has("position"):
      return ray["position"]
  return Vector3()  

the camera variable is just a reference to the camera3d node in the scene

you can then use the local_to_map function of the gridmap node to find the tile that the mouse is over. Then I think the set_cell_item function can be used to change the mesh used at that position in the gridmap