Use pyenv. However right now, it needs some packages that might not be available on the 64bit version.
Waiting on 64bit packages for llvm. These are needed for making Python from source.
Get the normal python and python3 pip from Cygwin packages.
Note that there is bug with Cygwin 64bit: http://stackoverflow.com/questions/18947163/uuid-python-import-fails-on-cygwin-64bits