I think your response was pretty good. I'd have gone with a similar retort of "Wow, I bet you have a lot of friends." So "Wow, you're nice" is a pretty perfect response in my opinion.

Don't dwell on it. He's probably already forgotten that he said it. Unfortunately, there are plenty of socially retarded jerks and he possibly said it in an attempt to be funny (as opposed to wanting to be unkind).