Hi Bo,
There are heaps of things to do in Perth but you should definitely take your kids to Heathcote Reserve. It is in a suburb called Applecross and it has the most incredible playground for kids. It is in the form of a massive pirate ship with heaps of different levels that the kids can access via ladders, stairs and ropes. There are lots of walkways, hidden passages, cubby holes etc to keep them entertained for a long time. BBQs are available and there is a cafe there too.
Kings Park has heaps of fantastic playgrounds also for kids. Stickybeaks would be my recommendation for your kids (3.5 and 6.5 yo).
You can hire family quad-cycles at the Point Fraser Reserve (about 1.5-2 km from CBD) and cruise around the river on the cycle paths. You can hire kayaks at the same location (2-seaters). These are good value.
I'm taking my boys to Margaret River in a few weeks time. We'll be doing archery, the maze and the cave tour while down there. The archery park also has mini-golf (ph 9755 4322). We have not been to the maze before but have heard great things about it. The caves are awesome. You'll have a great time there.
If you like a beer or two, I recommend Colonial Brewery, about 5-10 minutes out of Margaret River. It has a large playground for the children so they are entertained and you can stay longer
.
There is lots more but that is a start for you.
Have fun in WA.
Cheers,
Dan