What is the best stereo option to replace the factory stereo in a 2006 Nissan Maxima 3.5 SL? Estimated cost?

The "best option" depends on your budget. You could easily spend more than the car is worth on the "best" stereo system. Name your max price and we'll narrow it down for you. 

Crutchfield.com.                

Nissan dealers sell reconditioned stock stereos. That's your best option unless you buy the kit that runs the climate controls when the stock radio is replaced with an after market stereo.

Well you don't say what's wrong with it.Maybe it's just a blown fuse which would only be a couple bucks.Being 14 years old i would not spend much on fixing it.You could take it in to a car audio place where they install stereos have it fixed but I would just go to a wreckers and pick up a used one so it fits in properly without having to do modifications.