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.