What would be the best way to skin a hollow tube with bones?

As shown in the screenshot, I would like to skin the brown tube model with the white colored spheres ("bones") in such a way that when the spheres move, they in turn deform the surface of the model:

I have tried out Geodesic Smooth Skinning as well as Linear Blend Skinning on the model, but upon deformation at run time, there are a lot of rough edges at certain places (the spheres are hidden):

Is there any other way to help make the model smoother upon deformation at run time? Any help would be greatly appreciated as I have been stuck on this problem since quite a few months now :)