Try Trinity Place Shelter in Harlem
They are very small but they might be able to refer you
Trinity Place Shelter for LGBT Youth, Morningside Heights - Harlem One Stop
Also - New Alternatives has an emergency number for housing referrals
New Alternatives » How can I get help?
If you are having an emergency on a day we are not open, or need a shelter referral,
call Kate at (718) 300-0133.