Web Template:
When a user who has design rights customizes a website in the user interface (UI) or in a web-editing application, such as Microsoft SharePoint Designer, and then saves the website as a template, a web template is created. Web templates are stored in the Solutions Gallery of the top-level site in a site collection, where they become available for subsite creation on all websites in the site collection.
A web template is persisted in the SharePoint database as a Microsoft SharePoint Foundation Solution, which is a file that has a .wsp extension. The .wsp file is stored in the Solutions Gallery of the site collection.
Site Template:
SharePoint site templates are pre-built definitions designed around a particular business need. You can use these templates as they are to create your own SharePoint site and then customize the site as much as you like. You’re probably familiar with the default site templates, like Team Site, Blog site, and Group Work Site as shown here.
In addition to the default templates, you can create your own site template based on a site you’ve created and customized in SharePoint. This is a powerful feature in SharePoint that allows you to create a custom solution and then share that solution with your peers, the broader organization, or outside organizations. You can also package the site and open it in another environment or application like Microsoft Visual Studio and further customize it there.
Site:
A site collection consists of a top-level site and one or more sites below it. Each top-level site and any sites below it in the site structure are based on a site template and can have other unique settings and unique content. Partition your site collection content into separate sites to obtain finer control of the appearance, content, and features of the various pages in your site collection.