Face it - no one really cares where your team allegiance lies when the Yankees with the World Series. You're in New York, and the Yankees/Mets/Rangers (and so on) run supreme.
Lesson #6 in moving to a big city: You can't just turn on or off your sports allegiances based on location. Just realize that you will be bitter if your hometown team doesn't do as well as your new town team. It takes time to develop feelings for these teams - and I've noticed many 'transplants' never do let go of their hometown team love. For me, I'll be happy if I'm able to retain my devotion and add a few NY sports teams to the mix as well. I will say, though - as much as I am bothered by bandwagon fans, it's hard to not get caught up at least a little in the excitement of an entire city celebrating a championship.
Plus, the poor Yankees have had such a rough century! They deserve a win more than any team. (please, please sense the sarcasm there. Normally I'd assume one would, but with a statement as bold as that, I've got to cover my bases....no pun intended.)