not sure the blue mountains would hold much allure for your autistic LO.
Sydney has loads for kids in the city.
In September it will be too cold to go in the sea but you might get some weather nice enough for the beach and bits of paddling. Clovelly is by far the most family friendly beach (it's near Bondi in the Eastern Suburbs). There's safe paddling as it's so sheltered. There's a cafe but it's not especially family friendly (they tut tut at pushchairs).
I agree that Taronga zoo is good but it's also very hilly so depends whether that's a problem. Darlign Harbour has both the Aquarium (which is excellent) and Wildlife World, which might be enough for you as you can see koalas and kangaroos and all of those things.
If you are hiring a car I would recommend Featherdale Wildlife Park, about 45 mins drive or so from the centre. You can actually pat the koalas and feed the kangaroos and it's much more laid back than Tarongs, even if it doesn't have the same great view.
There are some nice outdoor pools but too cold at that time of year. The pool at the Olympic Village is excellent for children and has two family changing rooms. There are number of pool areas ranging from shallow paddling to water rapids so would suit your children well. The only problem is that I always found the Olympic pools quite chilly at that time of year (despite being indoors) and we never lasted more than an hour (which might be sufficient for you anyway). Again you need a hire car to get to the Olympic Village (it's at Homebush).
Centennial Park is lovely for kids - has some playgrounds and used to have a good cafe but they were refurbishing that when we came back to the UK (Jan 08 therefore might be finished now). There are lots of cockatoos waiting to be fed if you can spot them!
The botanical gardens will be a hit with your 4 year old once she spots the flying foxes hanging in the trees near the cafe!
Other beaches worth a mention include the harbour beaches at Watson's Bay (shallow paddling, nice fish and chips!) and Clontarf (good playground next to the beach but it's on the north shore so you need a car).
If you go to Coogee Beach you'll find a great new playground up the hill at the south end of the beach (follow the cliff road away from the beach and past the swimming pool) though it's not fenced and might be a problem for you in terms of keeping an eye on both kids. There's a cafe nearby called Barzura which does great breakfasts and is family-friendly.
There's also a playground at Maroubra beach (which is fully fenced) with a snack bar nextdoor doing good coffee while you sit on a bench and watch the kids.
Hope this helps. Anything else let me know!