I can't think of a better way to isolate potential future fans and surround yourself with a few hundred Red Bull supporters suddenly pissed that you showed up to root for the other team.
I really like the Terminus Legion's (Atlanta's new SG) strategy. Commit to a name, be cool people, host fun events, get some scarves made, and organize. The goal here should be winning over new fans and fence-sitting Red Bull/Cosmos fans itching for a true New York MLS team.
Call yourselves NYCFC Supporters, arrange a first meeting, elect a board from everyone who attended the meeting, and set up regular meeting times. Get yourselves a president, secretary, and treasurer. Then get in touch with the more approachable supporters groups in MLS. Try the Timbers Army. They are crazy sons of bitches that get a diverse group of a couple thousand men and women showing up for every damn game. TA's informal motto is something like, "if you think you want to be in the Timber's Army, you already are." By all accounts, they are very cool people. Arrange a conference call with your board and a TA rep and start asking questions. Or get in touch with Terminus Legion. They're new too, but very organized, and might be willing to help out another new group.
Also, try to be nice, welcoming people. I know it's not totally apparent here or on Facebook, but not many people actually know about this team, and fewer know about the supporter's group. From what I've heard, Viking Army/Empire Supporters are a bit insular and tough to join as a newbie. NYCFC Supporters should be the alternative. I'd save the arena invasions for when there's a derby and we actually have a team to show for it.