If you go to Caversham Park then take your swimmers with you. There is an outdoor pool area and picnic area on the otherside of the carpark. Might be a bit cold for swimming but if you get a warm enough day it would be good for a paddle.
There are also old trains and tractors to play on too.
Bunker Bay is lovely. You can do some shopping in Dunsborough and spend time on the beaches there. Very, very safe for toddlers as the water is very calm, warm and not very deep.
Busselton is worth a visit and a walk along the jetty - if they've finished the renovations though.
You can visit Metricup bird park. Small family owned place. Very informative and good for all the family.
Fudge factory and chocolate factory are good too.
Simmo's ice cream is also worth a visit - big play area there too.
As for wineries/breweries to visit with a toddler, we've always gone to:
Occy's. Between busselton and dunsborough. Good brewery and they have a play area and small toys. We stop there just to stretch out legs for half an hour or so before heading further South.
Bootleg brewery is good for food and play!
Wise Winery is my favourite. Spectacular food and the most amazing views. Play are for children but not up top where the restaurant is - that said....it is special!
Anyway, I am wittering on now and you may already have your plans but these are just some of the things we like to do when we head South.
Let me know if you need anything else.
Have a great time!