First, make sure you have the latest software updates:
http://developer.apple.com/java/
Then, open the Java Preferences Application (in /Applications/Utilities/Java folder). There you can set the default version Java version. For more information, see:
http://developer.apple.com/java/javaleopard.html (scroll down to "Run Multiple Versions of Java")
Update: Jet Profiler for MySQL is now available as a mac dmg installer which automatically detects and uses the correct Java version. You no longer need to do any manual configuration. (but you still need the latest Mac OS X Leopard on Intel 64).