I know that many banks in NYC are not accepting this new NYC ID as a primary source of identification. That being noted, is it okay for banks to accept this NYC ID from a non-customer for the purpose of CTR filing (as the CTR conductor)? How are your institution handling this matteR?

The "rule of thumb" is that the ID should be of the type that you'd accept for check-cashing. If your bank won't accept the ID for check cashing, you probably shouldn't accept it for CTR purposes.

That said, if it's the only government-issue photo ID the individual has ....