Asking what's the cheapest car rental in Costa Rica is kind of a loaded question.
If you truly want 'cheap', you're going to get junk; at best poor customer service and at worse, an undependable vehicle that you're either too embarrassed to be seen in, or (sometimes) seen pushing to the next service station...
I think what you're asking for is 'reasonable' or 'fair' amount to pay for the use of a car during your vacation.
You can go with the big box rental stores like Dollar, Alamo, Budget or chose to see more local color by using a 'native' agency.
I chose a company based on customer reviews more so than just the bottom line dollar amount. It's my vacation, I *should* enjoy it and not worry about the fact that I already over-paid for the airline ticket, the parking, the baggage, the airport food, etc. Get the point?
I got to enjoy my stay without the hassles of a bad car on top of it all. I recommend, and so do a lot of others, Vamos4x4.com for their 'what you see is what you pay' attitude, not 'oh by the way, it's going to be X amount for this, this and that." I like to know where I stand *before* the end of the rental.
Something else that's nice is that you can get a quote from their website without talking to anyone or making a commitment.