Having been to both countries, I would prefer Chile over Costa Rica.
Costa Rica is fast becoming an American tourist trap with most of the worthwhile sights set up to extract as many dollars as possible. When we traveled in Costa Rica, we could not even opt for public transportation between cities because it would have taken three times the hours as the pre-arranged "tourist mobile". I am not sure how far out of San Jose you would get, but the places we went I would have little desire to return to.
While visitors to Chile are on the rise, it certainly does not feel overrun with tourists. The food is good and Santiago has a lot to do, a nice subway, and is relatively safe by South American capital standards. You can also easily get buses from there to other nearby places like Vina del Mar and Valparaiso on your days off to get to know them as well. While it does suffer from smog, I have to say that it has improved dramatically from the first time I went in 1999 to the last time in 2009. I was also there in June, the coldest and smoggiest time of the year and I did not find it unbearable.
What may help you is to indicate what you are looking for in particular in the given country. Certainly we can find several people recommending one country or the other since 75% of travel advice has to do with personal preference.
As to Amelia's comment above, it seems as if the OP has to choose between the two capital cities. As for stray dogs, I was in Valparaiso as well as Santiago and saw many more stray dogs in Valparaiso. :-).
Edited by: quinella66