Is usr/local/bin the correct directory to place JAR files?
From a SIP perspective, /usr/local/bin is perfectly fine to place JAR files.  

SIP excludes the directories:


/usr/local 
/Libraries
/Applications 


Anything in these directories can be read/written/executed.  Which one of those makes more sense for you to place your JAR files is entirely up to you.  (IMO), since it is a run-time and presumably it's part of an application, putting it in a sub-directory within the /Applications directory is not a bad place to start.