Good way to document controller actions in PHPDoc?

I don't really understand your problem/question. You can put whatever you want to in a phpdoc block, including the relevant URL for a controller action (you can even use markup if you want):

/**
 * This is some foo action.
 *
 * URL: /foo/bar/baz
 */
public function fooAction(/* ... */) {
    // ...
}

That said, if you specifically want to use a custom tag like @url or something, then you just need to use the -ct command-line option to tell phpdoc that you don't want it throwing parse errors when it comes across your custom tag(s):

# Will specify custom tag @url
phpdoc -ct url ...