Neither of these is natural.
'Where are banks?' is very strange. 'Banks', without an article, refers to banks in general, or all the banks in existence in the world. This is an odd concept in the context of asking directions. Nobody would say this, and the listener might be confused.
'Where are the banks?' sounds better, because it's more specific, but it's still a little odd. 'The banks' implies all the banks in the city, for example, and suggests that all the banks are in the same place. Or that all the banks have suddenly vanished overnight and you're wondering where they are!
As you only need one bank, a more natural question would be something like 'Could you tell me where the nearest bank is?', 'Do you know if there's a bank round here?' or 'I'm looking for a bank. Is there one near here?'