I'm a cinnamon-raisin partisan, but I'll admit I was brought up short when I learned in Jacob's piece that they were invented by <spit> Lender's.
Here's a 1952 New York Times article that treats bagels and lox as an exotic delicacy. It dates from just a few years before the cinnamon raisin bagel was invented. 
And here's a 1951 NYT theater review which assumes that the readers need the words "bagels" and "lox" explained to them.
As recently as the fifties, then, NYC bagels were an obscure ethnic food. If you're claiming bagels as a NYC tradition, rather than specifically a Jewish tradition, cinnamon-raisin was present at the creation.
(Bonus Weirdness: The Times sent a reviewer who didn't speak any Yiddish to review a Jewish comedy show, and then panned it because he didn't understand the jokes. In 1951.)
