I am planning to book an open jaw ticket for my trip to South America. Planning to fly into Buenos Aires and out of Santiago Chile. I understand that i will have to pay reciprocity fees when enteringBuenos Aires, but was confused whether or not will have to pay the fees while exiting out of Santiago airport?? Also, are these fees charged even if you take a domestic flight from a city in Chile to Santiago airport??

Let me be more specific with my question.
On my arrival, i will be paying the reciprocity fee in Buenos Aires and then will be entering Chile via Boat (Lake crossing) and then eventually taking a domestic flight to Santiago to spend a couple of days and then eventually fly out of Santiago to New York. In this scenario will i be subject to any reciprocity fees in Chile on exiting the country?

You're fine. You pay Chile's reciprocity fee only when you arrive in the country internationally at Santiago airport. Entering Chile by boat, no. Flying domestically to Santiago, no.

You might have to pay an airport tax ($20 or so) upon leaving Santiago. It depends on if your airline already includes that tax in the price of your ticket or not. But you're free and clear from Chile's reciprocity fee in this case.

Thanks a lot Jeff..Do you know of any travel agents who can put together a custom made itinerary for me for a reasonable price for Budget Travellers??

I responded to your TA question on your other thread -- try Alta Tours in California or search for Isabel on this board. Either should be able to provide a custom itinerary at reasonable prices. Realize that Chile is not an inexpensive country to visit.

Piya only to congratulate you for choosing Cruce de Lagos going into Chile,it is so beautiful,

When you cross the border into Chile by bus from Argentina, as part of your Cruce de Lagos, make sure you retain the slip of paper the Chilean border agent gives you. He didn't say anything about it nor did he attach it to our passports. You'll need it to exit Chile so make sure you hold on to it.