Hey, I was in a similar boat not long ago. Once I hit senior year of CS at University of Washington, not knowing Linux became not an option, particularly with Java. Honestly, it doesn't matter which way you go. I'm partial to Linux Mint for new users though. It's based on Debian (like Ubuntu) but is MUCH more user friendly. In many ways you'll feel right at home.
A couple things to note, to install programs, you don't download **** like you do in Windows, go into the menu (start menu basically) and go to "software manager" and search for the software you want and bingo, installed for you, free of charge! In fact, you can search just types of software, no trouble at all.
Also, reading a guide on emacs might be a good idea for small edits in Java code. You'll be running java stuff in the terminal (command line). It'll look something like this for a hello world program in the terminal
javac HelloWorld.java
// the above compiles the file
java HelloWorld
// runs the file and it uses the terminal as your "console" basically.
if you have a problem though you can type
emacs HelloWorld.java
and open a pretty awesome editor (though I'll personally not use anything but eclipse for building programs because it's familiar. VIM or emacs buffs will talk your ear off about why Eclipse is inferior, but Google employees using eclipse and cranking 200k will laugh all the way home).
Good luck! And check out the linux mint forums. Again, it's meant for noobs so people there are SUPER helpful and won't flame you for "dumb" questions usually. (there are ***** everywhere though so take that with a grain of salt)