Is this a reasonable summary of your question?
You have made a python app on the Raspberry Pi using the pi3d library and would like to run it on a windows machine. You looked at the instructions for getting pi3d to run on windows and ran into problems or just thought it would be easier to package the app in a windows exe. You looked at the introductions for py2exe and pyinstaller and decided on the latter, tried to install it on your Raspberry Pi but got an error message at some stage?
I've not used pyinstaller but their FAQ says that it only works on windows. But thinking about it, if you are packaging something to run on windows, starting from the position of having it already running on windows is probably a good idea!
Which comes back to the issue of setting up pi3d on your windows computer. This basically requires installation of python and then the modules: PIL (Pillow), numpy, pygame and the pi3d source from github. It also requires you to find the two gpu dll files and edit the constants.__init__.py file to point to them. (If you packaged your application as a windows executable not only would you have to find the correct versions of these files (there were several on my computer and half didn't work!) and put them in the package, you would also have to include various microsoft runtime interpreter dll files, prossibly requiring you to have installed visual studio etc.)
So the first step, even if you want to make an exe eventually, is to get it all running smoothly on windows. Let me know what problems you run into.