How can I disable pop-unders when using Chrome?

Yes,

but you need to block all scripts on a domain using Chrome's own script blocking feature.

Why?

Pop-unders are usually via JavaScript. In order to disable them, I block javascript on the specific site using the extension ScriptNo Chrome's build-in script blocking in:

Settings → Show advanced settings → Content settings → JavaScript → JavaScript Exceptions

At the moment Chrome's API do not allow proper script blocking which is also why Firefox' NoScript developer has not yet ported his extension. Third-party extensions like ScriptNo suffer from the same problem.

The lack of needed API can allow scripts to still load the first time you visit a website.

By design there is no option for extensions to effectively block scripts like in Firefox, therefore the only way to stop this behavior is to block all scripts on a domain using Chrome's settings which I mentioned at the top.

Chrome allows you to set preferences for EACH specific site.

Click on the icon in the browser.

Opens a window allowing to set Java and so on specific to that site.

Now to the pop-unders.

I personally use the Chrommes Poper Blocker extension.

It works for me, but then I have not visited your websites.

Poper Blocker 1.69 Blocks all these annoying popups and popunders that pop no matter!

If interested, get it here:

https://chrome.google.com/webstore/detail/poper-blocker/bkkbcggnhapdmkeljlodobbkopceiche