First of all, your son probably like the smell because he associates it with his uncle, whom he loves. I wouldn't read more into it than that.
Maybe his uncle could talk to him about smoking - how he knows it's terribly bad for him, what it is doing to his body, but also how hard it is to quit, which is why he should never start. (My dad, who never did manage to quit, had similar chats with my brother and I when we were kids. Neither of us smoke.)
If you share this with the uncle, it might give him the motivation he needs to try to quit. If he loves his great-nephew, I doubt he'll be happy to discover that because of the association with him, your son now likes the smell of cigarette smoke. If he's careful enough not to smoke in your house or around your child, he'll probably be horrified.