I personally prefer native PHP extensions. They are way faster than any other 3rd-party lib - depends on your task, but that is generally the case - and I get all the control I need over the document. DOM is the one I mostly use.
The best 3rd-party lib I have used so far, anyhow, is FluentDom; it provides a jQuery-like interface to navigate through the elements of the document and it may be installed using Composer.
I would not use regular expressions, unless I had to apply a really tiny change for which creating a new instance of
DOMDocument would seem like a waste.