The MonoDevelop that I got with Unity 4.3.4 doesn’t have a JavaScript class option.
Open MonoDevelop and with the Solution window open, right click on Assembly-CSharp and choose Add->New File. A new window will open up. On the Left side of the window select Unity. Then choose Unity Script, Name the Script and select New in the bottom left. It should create a .js file and place it directly in your assets folder of your project.