If you use Outlook/Exchange to setup meetings, I'd just setup the meeting in his office, make sure notifications are sent (including the location), then briefly tell him in a mail, via the meeting notification, a chat messenger or personally depending on how soon the meeting is and how reachable your boss, that you scheduled the meeting in his office for lack of other rooms. Ask if this is okay or whether you should reschedule to another time or whether boss wants to kick out someone from the official meeting rooms.
This assumes you know your boss's office and know that it is suitable to hold three people, your boss does use it occasionally to meet with people, and it has everything you need for a meeting, e.g. a whiteboard or whatever you might require. If you have doubts about that, ask first.
Basically it's about probability. The more likely you think the boss' office is an okay location for a meeting, the more you can first setup and ask questions later and the less sure you are, the more likely you should ask first before you do anything.