My DD is in prep this year so we have just been through the choosing. Or rather many of the people I know have agonised over the decision while we have a great school 5 minutes around the corner so I went with that. As your DS gets older you will be able to see if there is a particularly environment that would help him thrive. We have about 6 public schools and 3 catholic schools near us and some of my friends went to the open days at about 5 schools and then interviewed the principal of each to make a choice. it can be really confusing. things people might look for are -

1. large school vs small school eg. pros for large are more funding for specialist programs and more ability for kids to be put in an alternate class if problems occur vs pros for small schools - not so many kids in the playground
2. skills/interests of child - one of the mums and her dh sing and play guitar so they were interested in the music program of all schools.
3. school community - looking at the fetes activities is a great way to see how people work together.
4. bullying policy is interesting one - a friend had her child in a scholl with a great bullying policy but it was not put into practice, so best to ask around about that type of thing.
as the others have said - there is a long time to go yet. In your child's kinder year you will have heaps of opportunities to talk about this and research as much as you want. as with lots of things, gut instinct can come into it alot too.