Places I've been to where the pizza has been great:

Il Padrino's, Northbridge
Da Vinci's, North Perth
Pizza Bella Roma, Fremantle
The Moon Cafe, Northbridge
Portofino's, Hillarys Boat Harbour
Little Creatures, Fremantle
Delizioso Cafe in Subi, and at Carillon City
Empire Pizzeria in Glendalough (Jme will back me up on this one, he is a fan)

I haven't been, but Ciao Italia in South Perth gets a lot of rave reviews.

If you want to DIY, Vastese Bakery for the best pizza bases in WA