It's an improvised weapon.
It's not improvised in the sense that it's not designed to be thrown, but it IS improvised in the sense that a wooden toy ball is not a weapon. You take a penalty when trying to use things that are not designed to be weapons as weapons, even when you're only trying to do nonlethal damage, unless you've got a special ability (like the Throw Anything feat) which says otherwise. A baseball would be an improvised thrown weapon too, if you were trying to deal damage with it.
This has no bearing on how proficient you are with the item in its intended use. You could earn a living by taking the skill Profession (baseball player) and be very good at throwing a ball in that context, even though such a skill is no help in throwing a ball in combat. In much the same way, the Profession (lumberjack) skill makes you great at cutting down trees with an axe, but does not help you when it comes to fighting monsters with an axe (not even tree monsters).
As a final note, even if you had a ball which was designed to be used as a weapon, it would not be improvised, but you would still have to be proficient with it as a weapon to avoid the -4 nonproficiency penalty. If your GM ruled it an exotic or martial weapon, getting that proficiency is probably not worth it.