Unspoken, they mean pretty much the the same thing. But when spoken, the emphasis would typically be different, and that can produce a difference in interpretation because it makes the "too" or "also" agree with either "surprised" (first form) or "you" (second form). So:
"Are you also surprised?" could mean what it does in the following:
"So, you're angry, and you're upset, and you're frustrated. Are you also surprised?
"Are you surprised too?" could mean what it does in the following:
"Well I'm surprised, and Paul is surprised, and I'm pretty sure Betty is surprised. Are you surprised too?"