Hi, you might measure or look up but I think you have ~100mm of height to play with for CPU Cooler.
Scythe Shuriken or Shuriken Big will fit and probably cool the CPU unless you have plans to over-clock it. Not sure how quiet it would manage to be under extended load though, if you're planning on subjecting PC to that, video transcoding maybe?
Also look at Thermalright AXP-140 and Cooler Master Vortex Plus come to mind. Know little of the CM VP but 4 direct touch heatpipes should perform at least reasonably well.
No doubt there are many other options too, avforums worth a look as this question of which heatsink for Antec Fusion case no doubt asked many times. Pick the biggest/best looking lump metal and then experimant with good/quiet fans!
Ninja Mini, if you can get one anywhere.... would fit.http://www.silentpcreview.com/article754-page5.html