Hi!
I'm not a native speaker of English, but I consider myself fluent and I've lived in the US for almost 2 years - so I guess I know a little something.
From my experience, I wouldn't say the word 'funny' is a bad word, but it's one of those words that, depending on the context (or the way you say it, for instance), that it might sound like criticism.
If you are talking to someone you know, and this person tells a joke or does something funny, then it is no problem to say that he or she is funny. But if it is someone you are not close to, maybe it's best to keep it to yourself, since you don't know whether the person will perceive it as a compliment or not (especially these days when people get offended so easily). Maybe you can use the word ENTERTAINING instead: "You are very entertaining!".
Dear native speakers of English, what do you think?
:)