I suspect this is my ineptitude in getting path variables set right, but I\'m at a loss.
I\'ve installed the aws cli using pip in cygwin.
pip install aws
Thanks to matzeri in the comments above for steering me to the fix.
The problem was that cygwin had it's own python version... but not pip... so when I used "pip install" in cygwin to install awscli, it was the windows/anaconda pip. the solution didn't involve fixing paths, as matzeri pointed out, it would never resolve that with paths... it was these two lines...
python -m ensurepip # install a cygwin pip
pip install awscli # to install awscli for cygwin