Correct way to integrate jQuery plugins in AngularJS

Yes, you are correct. If you are using a jQuery plugin, do not put the code in the controller. Instead create a directive and put the code that you would normally have inside the link function of the directive.

There are a couple of points in the documentation that you could take a look at. You can find them here:
Common Pitfalls

Using controllers correctly

Ensure that when you are referencing the script in your view, you refer it last - after the angularjs library, controllers, services and filters are referenced.

EDIT: Rather than using $(element), you can make use of angular.element(element) when using AngularJS with jQuery