What works for me with Hugo (because I'm already using these tools all day anyway) is to keep the site in a Github repository.
Then when I make a change it triggers TravisCI to do a full site rebuild. (Takes longer to install Hugo than to actually run it)
Then once it's built, Travis has built in support for uploading to S3, and away we go.
Doesn't work for everyone, but it's really smooth and simple for me, I can even just go to Github, create a new page, and save it right there from the site. Which means I can edit from any device I want.
