I’m a little biased and use bash 
if you want to run it on the server itself I’d suggest https://github.com/lukas2511/letsencrypt.sh (which has few dependencies and runs nicely in bash).
Alternatively I’d use https://github.com/srvrco/getssl which is again a simple bash script that can be run on any linux computer and remotely connect ( via ssh) to automate the process - hence relies on nothing more than an ssh connection to the server. ( I wrote this one with the specific purpose of automating deployment on severs where I couldn’t / didn’t want to install anything.
If you want a full list of alternate clients - see List of Client Implementations