I think in this sentence both es (verb ser) and está (verb estar) can be used, but es is preferred.
Normally, when indicating ownership or delivery for something, we would use es:
This is for you.
Esto es para ti.
But when something is in a place or spot for it to be used then we use estar:
Why is the pen in the drawer?
¿Por qué está la pluma en el cajón?
In your example, if the message is written in paper taking a spot, then you can say:
Este mensaje está para el jefe.
But if the message is something that is moving around, then it HAS to be:
Este mensaje es para el jefe.
Other similar cases of estar:
I'm here to serve you.
Estoy aquí para servirle.
The book is in the office.
El libro está en la oficina.
Another usage when you can use both ser and estar is when you are indicating a purpose:
The pen is meant to be used.
La pluma es para usarla.
La pluma está para usarla.