I use Dynu.com as my DNS provider (they're cheap, provide APIs and very fast to update which is great for home IP addresses that may change). Then, to get the certificates, I use https://github.com/acmesh-official/acme.sh which is a shell script that supports multiple certificate and DNS providers. Copying the certificates to the relevant machines is done by a custom BASH script that runs the relevant acme.sh commands.

One advantage of DNS challenge is that it can be run anywhere (i.e. doesn't need to run on the webserver) - it just needs the relevant credentials to add a DNS TXT record. I've got my automation wrapped up into a Docker container.