"It is a good mannerism to reply for a message".
Is this sentence right? If so then why? Which one should be used in the above line — "good mannerism" or "good manners"?
The sentence you're looking for is:
It is good manners to reply to a message.
The phrase is "reply to" and not "reply for", but I guess your confusion is between the word "manners" and the word "mannerisms". They mean different things:
manners (or good manners, always plural) refers to etiquette, things that are considered polite, or expected in society. (You already know this meaning.) Example: "It is good manners to reply to a message."
mannerisms are idiosyncrasies or other peculiar behaviour specific to a person, his/her style of doing things, speaking, etc. Example: "Rajinikanth is a star mostly for his mannerisms."