Yeoman is a generator tool, helping developers create new project and solution directories. You'd use npm to get individual packages, and you'd use Yeoman to generate a new SharePoint Framework project, which in turn would fetch the correct npm packages and other dependencies.
Microsoft has published a Yeoman generator for SharePoint, which includes all the necessary workflow actions to create the SharePoint Framework base project. This way, developers do not have to start each project from line 0, trying to figure out what goes where. As things evolve and change, the Yeoman generator for SharePoint will be updated and new projects will simply get updated project structures and updated npm packages.
Think of Yeoman as a tool that provides you with access to a pre-defined checklist and build file for constructing your project base. You will typically install Yeoman with npm, as Yeoman is published as an npm package.
Yeoman is used with the...