There is no place in scripture where John would be considered effeminate.
There is also no place in scripture where MM is present at the Last Supper or was known as one of "The Twelve Apostles".
There is quite difference between an Renaissance artist painting a young man in the style which is contemporary to the period, and re-writing the known and accepted theme of the artists subject matter ( especially regarding religious messages ).
Imagine this; I am an artist who has been asked by the Queen to paint Prince William and Kate Middleton on their wedding day.
Which will be more acceptable ? Painting Prince William with rosy cheeks and having Kate Middleton showing a bit of cleavage.
Painting Kate getting married to Darth Vader ?
Do you get my point? An artist is telling a story, and painting it for his contemporary audience. It is one thing using artistic licence to add creativity and individuality, but to change the story to something completely different just might not go down too well with the patron paying the bills ( or the paintings other viewers for that matter ).
As Caelum states above, this isn't about who first painted John as being effeminate, but what the re-accuring themes and statements being made by artists during the Renaissance were.
Edited to add :-
Forget renaissance for a minute, i'm asking where the idea of a effeminate John came from.
Dave, I think Caelum has answered that question above. The answer is the idea of painting all the other effeminate young men portrayed during this period. You have to remember fashion and taste changes ( just look at the 1980's