Though I am not as experienced with JBoss I think your best shot would be to go with simple RMI.
In any case, go with Option 2!
What you are listing are basically the different types of packages War = web, ear = enterprise and ejb3.
They also specify where the config *.xmls have to be located and their names.
Would you require a session-based system where each connection could return a different set of values?
If so go with a Stateless SessionBean.
You can also have an MBean or a Service Bean, but they would only exist once.
RE: "Would you require a session-based system where each connection could return a different set of values?"
Thanks for the comments. I don't believe that it needs to be session-based. The java program returns a hashtable that contains the "result" (pass/fail), "message" (a note), and processing time. The hashtable structure never changes, but the values might change per each request.