does the civil court have the ability to issue a restraining order on
bank accounts in a municipal credit union in New York City?

You probably don't mean restraining order.  That protects one person
from being in proximity of another potentially dangerous person.

I believe you mean "attach".  Here, an excerpt from a legal site:

"Bank Attachments
Unlike some other attachments, freezing your debtor's bank account so
that they can not use or withdraw "their" money usually has a sudden
impact on the debtor. Even when the attachment does not catch any
funds, it can bring the debtor to the table for meaningful settlement
discussions."