Veja o matplotlib do sourceforge.
Há uma extensão de plotagem 3D simples - mplot3d
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The mplot3d toolkit adds simple 3d plotting capabilities to matplotlib by supplying an axis object that can create a 2d projection of a 3d scene. In the end it produces a list of 2d lines and patches that are drawn by the normal matplotlib code. Therefore the resulting graph will have the same look and feel as regular 2d plots.
Você pode verificar alguns exemplos nesse link para ver se funciona para você.