I think I found the link to the article
https://archive.nytimes.com/wordplay...sultPosition=3
I have subscription through work, but as I recall, you can access up to 10 articles a month for free (unless they have changed the policy).
At any rate, you kind of remembered correctly...it wasn't that the word gonfalon had not appeared in the puzzle at the time the poem was written...it's that the word is so obscure it has never appeared (at least up until 4/20/2009).
Below is part of the article:
I’m often asked, “Jim, how can I get my own name in a N.Y.T. crossword puzzle?” The answer is simple. First, do something remarkable. Second, be born with a name with a convenient combination of letters including lots of vowels. I should add one more option: have someone write a famously memorable poem about you. I’m sure Messrs. Tinker, Evers and Chance were a great COMBO but it’s the rhyme that makes them memorable a century later. That poem, called “Baseball’s Sad Lexicon,” is by the Algonquin Round Table regular Franklin Pierce Adams. First published in 1910, it’s still stuck in our collective unconsciousness despite one now-confusing metaphor.
What bubble is getting pricked, and ruthlessly at that? The word gonfalon has never appeared in a clue or as an answer in a Times crossword. It means a flag like you see hanging from crossbars in swashbuckling films, but in this case it’s a poetic reference to a baseball pennant.