What do you mean by "running the Web Services directly on Tomcat"? Tomcat has no built-in WS provisions, so whatever NetBeans does - it must be installing/using some
SOAP toolkit as well (I'm guessing that it uses the JAX-WS reference implementation, but I'm not sure about that).
If you're set on using an
IDE for this (personally, I've never seen the need for that), then I'm sure you can find plugins that work with Axis 2 as well; I know there's one for IntelliJ.