I have currently have both JavaBeans and Eclipse, but I switched to using Eclipse a couple years ago.
It probably doesn't matter much which IDE is used. For Eclipse, there are a couple metadata files with Eclipse project information (which are only used when the project is initially imported), but Eclipse will work with any Java code. If the code is edited with another IDE, it will still work with Eclipse. The only problem I could see is variation in the comment syntax. For example, comments starting with "TODO" are treated specially in Eclipse, although this can be configured on a per-project basis to work with any tags. In the end, all you are doing is editing text files.
I could see the NetBeans GUI editor being problematic, but that is only a problem if it is actually used. I don't remember how it worked exactly, but I remember that it generated code blocks which could only be changed with the GUI editor.
The compiler is completely separate from the IDE. I have been using the Sun JDK 1.5. Other compilers can be used for development, but it might be best to create releases with the official Sun JDK.
Eclipse is open source and can be downloaded at:
http://www.eclipse.org/