I don't understand the question here - the companion fare codes will still work (as long as there are 2 seats available) but the fare itself may go up significantly. So if you wait until March to book flights in June they might be more expensive than what they are now (though in general 3 months out is a good time for booking tickets barring some exceptions).

Or do you want to book 5 pax on one PNR while using the companion fare (I didn't even realise that was possible)?

I'd consider booking the flights without the companion certificate now so at least you'll be protected if the fares go up. You can always cancel and re-book later (the funds will be returned to you but will have to be used within a year of the original ticket purchase).

BTW: it seems unlikely to me that the flight will sell out to leave less than 5 seats available three months in advance. But obviously the fares will go up significantly the more seats are sold.