Want a peaceful, mutual divorce.

If there is no chance of conciliation then both can go for consent divorce.

I find it very hard to not been able to see my son who is just one km away from me and he is away from both his parents too. What should I do to get my son's custody?

I do understand what your are going through.  But be practical.  All this rona dhona dont do good to anybody, at least not to you, build up courage, think of what you can do legally to get in touch with kid.

You can file a custody case, but you wont get custody of kid until 7  years of age, at 7 kid will be asked whom it wants to live with, mom or dad then it balls in kids court.  Why you wont get custody is, Indian laws favor women, and kid is small, so it need to be with mom than with dad.   Practically too its not feasible to ask back kid than the wife, maintaining kid all alone and only with the hope that your parents would look after kid is a really insane thing to do.  Here too you are putting more pressure on old parents in their old age.  ITs not a puppy whom you bring home and tie to a cot, handling a kid all alone, for a male is very difficult.  Dont build dream house on your parents shoulders.

You can get visitation rights, but you have to make sure that you will visit kid and maintain good relation with kid for that d-day when he will be asked whom he wants to live with, mom or dad.  So plan accordingly.  Even here it wont be easy, once you file visitation rights case, your wife will not allow you to meet kid, all this will happen, and be prepared to roam to court everynow and then, you perhaps might have to give away your NRI status too, roaming to court is not a easy thing.  Chappal, aur gaadi ke tyre ghis jaayenge aur phat bhi jaayenge.

Does court still give my son's custody to my wife even she never was a good mother, not fed him breast milk, kept him away from  his father even I was just there and now she is in Australia and my son is in India? 

Sadly, Yes [80%].

 If my wife is not here would my in-laws be able to case against me of dowry or harassment which they said they would?

Take one day at a time.  Dont get tooo tensed.  Possibilites are N number.  

please do help.

 and peaceful divorce?

Divorce is never peaceful.  

It all appears so robotic. It appears to me that neither you were interested in this marriage from day 1 and nor was your wife.  You both seem to be put into the cradle by force and ended up making love and have a baby out of the wedlock due to some pressure cooker.  That being the case, it had to be like this only and nothing else.  You both got married  only because of your respective parents.  Marriage is life changer.  Before SSLC and PUC were life changers, nowadays its marriage.

Now coming to options for divorce, file divorce based on mental cruelty, and you will have a hard time to prove all of it and get divorced, usually it takes 7-8 years for contested divorce to get over.  If your wife has a grudge on you, it also appears that she has some deep grudge on you and your parents and for what her parents did to her by getting married her to you, you might have to face a number of false cases.  like DP, DV, 125 crpc etc. etc.  And one fine day you will get divorce.  Another option is to ask her MCD, ie mutual consent divorce.  Usually its done with one shot payment.  lumpsum as settlement money toward divorce, pay her money and in 6 months you are headache free.  So choose your options wisely.