Late Game is a good counter, since he practically doesn't have a teamfight.
But on a more serious note, I've always considered Shaco the premier counter jungler: His shtick is kind of "I don't get a late game, but I can damn well starve them enough that they don't get one either."
I don't know if it's still a thing or not, but there used to be a meme of "Your Shaco Feeds, Their Shaco is Korean and has 8 kills before you finish your first buff"; a good Shaco is pretty scary, and even now I have a habit of overreacting when I see the other team has a Shaco.
So I guess what I'm trying to say, I personally wouldn't blame you for having a tough time against a Shaco that knows what he's doing.
I honestly can't help you much; I consider myself a bad jungler, and have a tough time against counterjungling myself (Like, you take one camp from me, suddenly I've died 12 times. All at once), so I should probably just leave the discussion to people who actually know what their doing.
I would wager to say that having a jungler who is good in duels might help out; Lee Sin comes to mind, especially with all his reveals, and if you can't take him on, you can ward jump to safety.
EDIT: I guess it's worth mentioning you can see his smoke effect from Decieve from the fog of war, so keeping watch for that could help you track him down.
Actually, just having the 'jump over wall on demand' ability seems like it'd be useful against a Shaco if he only engages by Decieving over the wall. However, just because Shaco's that kind of champion, a sufficiently prepared Shaco might have just sent in his clone to invade you and freak you out, and the Real Shaco would be right over the wall where you'll escape to. But that's probably not something you'd see in your average game, Shaco still has probably the best potential to play mind games with his opponent.
That reminds me, I should look up a video of good Shaco outplays/mindgames/whatever-you-want-to-call-it.