Sometimes a person's answer is really helpful, but I'm not sure if thanking the person as a comment is appropriate (as it's not a discussion forum).
Vote for them!
That's the proper way of saying thanks.
You're spot-on though, we do like to keep the chatter down to a minimum as it makes it harder for people to find good answers if they have to wade through comments.
But it's unlikely anybody (users or moderators) would mind the occasional comment letting people know how good an answer is. As somebody who has written one or two answers and has had a few thankful comments in return, I can say it is nice to have personal feedback.
I think you should go for it, but save thanks-comments for the truly exceptional answers.