Hello M.. My sons are not teenagers but I have plenty of relatives who are teenagers. And from what I have experienced they will find something to be insecure about while everyone else thinks it's not a big deal.
My niece who is 15 wants a nose job because she feels her nose is too big. I'm constantly telling her their is nothing wrong with your nose! But, she does not believe me. I think if at least one of their peers make a comment on their appearance they are going to take it to heart.
I remember when I was that age I wanted a bigger chest and was very self conscious.
I believe that all you can do is reassure him everytime he makes a negative comment about his height. In the end two things will happen. He will eventually get taller (at his own pace) or as he gets older he will accept himself as he is and be extremely happy with what god has given him. I have accepted that I will never be a D cup.
This may sound wacky but I would do a search for famous people who are short and then tell him this person is not 6 feet and look what they have accomplished.
I tried this with my niece. I found pictures of a few girls who did not have little cute perky nose but who were very attractive.
Hope this helps a little.