What is LEGO Junior?
LEGO Juniors sets use normal LEGO System bricks.  In other words, they are exactly the same size as the "normal" LEGO bricks.  

However, the Junior sets are specifically designed for younger children.  They often have large single-use pieces (for example, for walls or frames), and are generally very easy to construct.  They also limit the use of small or difficult to handle pieces as much as possible.

Depending on how advanced your son is, my guess is that Duplo is the most appropriate.  If he no longer attempts to put toys in his mouth, and can focus/concentrate on a task for a decent amount of time, and has started developing fine motor skills, then Junior would probably be the most appropriate.  

For reference, LEGO labels the Junior sets as appropriate for 4-7-year-olds, but I have met only a couple 4-year-olds that I would give the Junior sets to.  Most 3-year-olds should probably be playing with Duplo.