SharePoint Site basically is a website. SharePoint allows us to create websites of specific types like Personal site, a Team Site, a social media site, a blogs or a Wiki Site etc.

On the other hand, a Site Collection in SharePoint is a collection of SharePoint sites that share common features like Content types, Templates, Site columns, permissions, Web Parts etc.

A Web Application is a collection of Site Collections in SharePoint OR in order way a site collection resides in a

web application. Normally a SharePoint web application is corresponds to a website in IIS means when a SharePoint Web application is created, it creates a WebSite and an application Pool in IIS .