It depends on what you want to see and why. For example, if you have a voucher for a free pass and you just want to use it then you can go to either. Or if you a visiting Sydney from overseas, then maybe you can buy a ticket for both at a discount (as at the counter or go online). Or if you particularly like marine animals such as dugongs, crustaceans, octopus, fish, penguins, then go to the Aquarium. Personally, I think its a bit boring now, I went once with I think my primary school class. Then a few weeks ago I went with my biology class at uni and it hasn't changed. There is a touch pool where you can touch empty port jackson shark eggs, sea urchins and other non-toxic small non-moving small animals, both live and empty eg shells (dead things would decompose). There is a part where the aquarium is a true tank, like a wall and you can watch all the fish and things in there. There are also coral and platypus.
To see reptiles, you would need to go next door to the Wildlife park. I haven't been there but I am not that interested. Go to their website to find out what they offer.