The correct answer is “May I come in, sir?”.
“May” is a modal verb that is used to ask for permission. In this case, the speaker is asking the permission of the person they are addressing to come into their room.
“Should” is a modal verb that is used to express obligation or advice. In this case, the speaker would not be using “should” to ask for permission, but rather to express that they believe it is the right thing to do to come into the room.
“May be” is a phrase that is used to express possibility or uncertainty. In this case, the speaker would not be using “may be” to ask for permission, but rather to express that they are not sure if they are allowed to come into the room.
“How” is an interrogative pronoun that is used to ask for information about how something is done or how something is. In this case, the speaker would not be using “how” to ask for permission, but rather to ask how they can come into the room.