What does this statement mean from a boss?

It's a type of back-handed compliment, possibly wrapped in a joke about the fact that everyone loves your work, and he's pretending they say otherwise, as a good-natured tease.   

He's a domestic terrorist.

He's kidding  you, and saying something good.

He likes you, I would take it as a compliment, or a joke. 

Laugh. It's just a smart-alec statement a lot of people think is funny. He's just joking with you. 

He's making a joke. Lighten up.

You were given a compliment and you want to complain?  When a person says "I think you're alright".............then stop worrying.

It's a weak form of humor.

That comment usually means he like what you do.

Its obvious.