BitFenix Prodigy ITX Case Fans

The stock fans are actually really quiet if you compare similar fans at 100% speed, but they aren't great for performance because they don't move much air and aren't positioned very well.

The rear fan isn't too bad -it's in a sensible location and the proximity to most coolers means it's going to be fairly useful. For maximum performance you'll want a 140mm in here, something with more of a performance leaning ideally, with some form of fan control. Being at the back, it's unlikely this fan will be the noisiest component.
For the front fan, the stock 120mm location is a bit useless as it just blows against drive cages. For high end performance a 230/200mm fan is going to be the best option but if you want to keep noise down then a 140mm is probably the way to go.

Ok, the unhelpful stuff. The Bitfenix Prodigy isn't the quietest case in the world, and never will be, because it's full of holes for ventilation - if you have the black/vented front version then it'll be even worse. It's a case with excellent airflow, but this is usually kinda counter intuitive to noise levels.
I find it unlikely that the two stock fans, even if they are running at 100%, are the loudest components in your case. If you've done a great job picking components specifically for low noise, then it's possible I guess, but unlikely. It's quite possible changing the fans won't really fix your problem.

Ok, onto vaguely helpful stuff.
Fan control is probably your biggest priority if you haven't already looked at it. Most fans at 100% speed are loud and any fans which aren't probably aren't moving much air. A dedicated fan controller is likely unnecessary, you can do a decent amount just with a single system fan header and a fan splitter to control two case fans. If you haven't already looked into this, I'd start here.
For sound proofing a Prodigy, there's not huge amounts you can do. As I mentioned before, if you have the version with a full mesh front then there's not a lot to block any noise coming out. Having said that, noise damping panels (available from specialist sites) might be an option as they are easy to cut to size and remove fan area(s). There's not much you can do for the side/top vents though - I'd advise against blocking these.