Blocking Chrome Extensions from running on my site

It's not possible. At the web server end, you are only only able to control what the browser will allow you to control. In simple terms, this means you can control the data (HTML, javascript, headers etc) that you send back to it. That's about it.

Can't you create a Content Security Policy (CSP) and block inline javascript and only allow javascript from specific domains? You could even create a CSP in report-only mode and collect violation reports via something like https://report-uri.io/