Several options:
Option 1: You can put it under your classpath (in Eclipse put it under and source folder), so you can access it via the Classloader: MyClass.class.getResourceAsStream("myproperties.properites")
Pay attention that MyClass must also be in the same source folder (actually it's a bit more complex, it must be in the same classloader hierarchy, but any class from the same folder will do the job)
Option 2: Put it in WEB-INF folder. It's a preferred option, since you don't need to deal with the classpath. You'll need a ServletContext to access it: javax.servlet.ServletContext.getResourceAsStream("WEB-INF/myproperties.properites")
In jax-rs you can obtain the ServletContext using the @Context annotation in any registered resource or provider.