Have sudo installed, have the user running the Java program entered in /etc/sudoers for the commands in question, and use sudo -u jim ls ~bob.
sudo -u jim ls ~bob
Problem solved. Used JSch (http://www.jcraft.com/jsch/) to SSH into the server with known username and password, and execute command. Thanks all for your suggestions!
Possibly a java implementation of Expect? ExpectJ comes up when googling but I couldn't find any documentation regarding running under 1.4.2.