Search Java jar (ear,war,...) files for class / method
I don't know about a standalone tool, but if you create a simple Java project in Eclipse and add the jar, war, etc files to that, you can use the "Java Search" search dialog in Eclipse.
This does exactly what your want and among others has an option to search for methods, and even allows you to filter those on references or declarations.
Alternatively you do have to build something yourself, although you could always use an existing tool as a start, like JavaClassFinder you mentioned or JBoss Tattletale.
I just wrote a small (OpenSource) text search utility for JAVA archive files. It can cover your requirement to some extend.
EAR Search can be downloaded from http://sourceforge.net/projects/earsearch