How do you find the following collocation?
Polite reminder
...let's say we have to send a reminder to our boss regarding the erroneous deduction in the salary.


Yes, you can use "polite reminder" that way, Tom. In other words when talking to someone about a reminder you are sending to a third person.

I wouldn't recommend using the collocation IN the reminder you send to the boss because it could end up sounding sarcastic, in my opinion.
It highly collocates as it stands, but whether or not it is appropriate for a message to your boss will depend on the full context.
 Yankee's reply was promoted to an answer.