To use certbot on Cygwin, install the python3-pip package using the setup from http://www.cygwin.com. Then install the certbot python package by running
pip3 install certbot
You can set up auto renewal by setting up a Windows Task to run every day with the action.
Program: C:\cygwin64\bin\bash.exe
Add arguments: -c "certbot renew -n"
Your certificate is store in C:\cygwin64\etc\letsencrypt\archive\