As some people already have said, it depends a lot on your personal taste. As a person that have used both Eclipse and NetBeans, I would like to try to share some experiences.
NetBeans - Abstraction to a higher level.
For instance, there are wizards to create web services and client artifacts. Generated classes etc are kept in a special place in the project, separated from your own code. Having generated a service, you can drag and drop a web service operation into your Java class and code that invokes the operation is generated for you.
- Better support for WSIT configuration files.
No manual editing needed, configuration can be done without reading, or writing, a single line of XML.
Eclipse - Better support for Axis 1 and 2.
- JAXB binding compiler plugin (XJC) available.
- Less good support for Metro and JAX-WS standard.
I had to write Ant-tasks for wsimport and wsgen myself.
- Generated artifacts are not treated specially.
Generated classes are mixed with your own classes, you can see "everything" in the ordinary project view.
- Web service test tool available.
Overall, NetBeans give a more "integrated" feeling. I may have missed some plugin for Eclipse that can aid in web service development, but on the other hand I did not need to look for something like that for NetBeans, since it was already present.