Do I have to wait till the end of the lease to file a holdover petition in NYC

Double check with an attorney whose practice focuses on landlord/tenant law, but here is my understanding - You can - and must - return any rent money you are alleging is a holdover. You cannot sue for holdover until the lease expires. During the time period covered in the lease, the tenant is a tenant. After the lease expires, the tenant is a holdover. The one thing you can do to ruin that is failure to return any rent money sent. I understand that you get an auto deposit, which presents a particular problem because you're not just returning a check, but find out now how to return it or - better yet - prevent it from being deposited once the lease expires. There are things you have to do before you can actually sue in court, i.e., issue statutorily required written notices that must be served in a particular manner. Consult with counsel to get it right.

If the tenancy is not a month-to-month but is for a period of time (e.g., one year), you do not need to serve a predicate notice to terminate the tenancy. Comply with the terms of the lease. If it is a month-to-month tenancy, you will need to serve a predicate notice to terminate it. You can begin a holdover action once the tenancy ends. Take steps to stop the receipt of money that will be auto-deposited. If it is auto-deposited, return it as soon as possible making clear that there is no tenancy. Retain a landlord-tenant attorney to assist you.

You should consider contacting section 8 regarding the auto pay and your decision to commence a holdover proceeding. You Should consult with an attorney regarding your matter.