Yes, "get you back" and "get back at you" mean the same thing. But the context means a lot when you use these words and you will find situations where they don't mean the same thing.
These two sentences mean exactly the same thing...
"You pranked me, I'll get you back!"
"You pranked me, I'll get back at you!"
When talking about romance, these two sentences have different meanings...
"You left me, I'll get you back!" - means the person will try to fix the problem and restart the romance.
"You left me, I'll get back at you!" - means the person will seek revenge because you left.
You notice that I finished my sentences with an exclamation mark (!). That's because the words aren't passive and they sort of demand that extra !!!!! at the end.