Jython or JRuby?
Anything you can do in one, you can do in the other.  
Learn enough of both to realise which one appeals to your coding sensibilities.  There is no right or wrong answer here.
It's a high level conceptual question. I have two separate code bases that serve the same purpose, one built in Python and the other in Ruby. I need to develop something that will run on JVM. So I have two choices: convert the Python code to Jython or convert the Ruby to JRuby. Since I don't know any of them, I was wondering if anyone can give me some guidance. Like which one runs faster, or more importantly which one has tools available for easy code migration(.pyc to .jar files)?