I am using MacOS 10.11 and in addition to the native Python installation I have installed Python and Pip through MacPorts. python and pip are linked against the respective MacPorts versions.
However, when installing a package via
sudo pip install <my-package>
a specific .so file of that package is linked against the native Python executable. More precisely the output of otool -L on that .so file is
/System/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.5)
whereas the MacPorts version of Python resides at
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/
How can I force Pip to use the correct Python version to link against?
The short version is: you can't.
It's not a problem with pip. The nupic package relies on the nupic.bindings package, which contains the _math.so you note, and it's currently distributed via PyPI as binary-only:
https://pypi.python.org/pypi/nupic.bindings
You can compile your own nupic.bindings package, but the build process looks fairly involved, which is probably why they distribute binary-only:
https://github.com/numenta/nupic.core
Good luck!