Those 3 locations (all at SUNY Downstate Medical Center in Brooklyn) are "representative of the types of properties that may be available following submission of an application by the relevant university/college and approval by ESD and/or the Start-Up Approval Board". So, you could work with any university in NYC, not just SUNY Downstate (although the campus is a really nice spot for startups as well!)

NYU Poly operates incubators at Jay St/MetroTech in Brooklyn and Varick St in Manhattan. Columbia has a biotech incubator (AUDOBON) in Washington Heights. Cornell has 22k ft^2 in Google's building in Chelsea. All of those sounds like they would qualify (if you could get the right people on board)