Toe puncher? That doesn't sound very pleasant.
You could always use a leg band? Some folks use zip ties instead. Just ensure it's not on too tight. But this is best for adult ducks, since babies grow so fast you'd be having to replace the zip ties frequently to prevent the duckling outgrowing it, which would be very uncomfortable for them.
So while they're growing, you may be better off marking them with food colouring, on the top of the head or legs. Just ensure you don't use especially bright colours, like red, as this may cause the other ducks to peck at them.
Depending on the duck in question, you may be able to tell him apart without any of this. If you know which it is now, you can already identify him anyway, right?