The home side rebounded before the halftime interval and pulled one back as Tom Biss followed up a parried effort from Futsal Whites player Dylan Manickum to get Waitakere going.
Mulligan pounced on a loose ball five minutes from the break to restore parity between the sides and when Boyens headed in from the set piece just after the hour mark, the comeback was complete.
Sean Devine's Canterbury side defended home turf as Tom Schwarz powered in a 28th minute header and Dylan Stansfield added an insurance goal to grind past a gritty WaiBOP side.
Canterbury's opener came as Schwarz, a member of the two-time defending ASB Chatham Cup winning Cashmere Technical side, headed in a freekick mid-way through the opening 45 minutes.
As they began the second half a goal down, WaiBOP saw several chances come and go as Sam O'Regan, former Canterbury United player Federico Marquez and Chad Coombes all had openings in the first 10 minutes but couldn't profit.
They were made to pay for those misses as Stansfield's header, from a Roussin Nkoy cross, provided a buffer the home side didn't need in the end as the visitors couldn't find a way back into the match in the final 30 minutes.