The way to use should still be the toInteger(), because it is not really deprecated.
int value = '99'.toInteger()
The String version is deprecated, but the CharSequence is an Interface that a String implements. So, using a String is ok, because your code will still works even when the method will only work with CharSequence. Same goes for isInteger()
See this question for reference : How to convert a String to CharSequence?
I commented, because the notion of deprecated on this method got me confuse and I want to avoid that for other people.