The aws command is
aws s3 ls --endpoint-url http://s3.amazonaws.com
can I load endpoint-url from any config file instead of passing it as a parameter?
This is an open bug in the AWS CLI. There's a link there to a cli plugin which might do what you need.
It's worth pointing out that if you're just connecting to standard Amazon cloud services (like S3) you don't need to specify --endpoint-url at all. But I assume you're trying to connect to some other private service and that url in your example was just, well, an example...