I think you have done everything right on the vSphere side.
What is the NetApp storage system telling you? Are you hitting any CPU spikes, back-to-back CP's, are you overdriving your spindles? What type of disks are you using? Any errors showing up in the messages file? I think your storage system is the most likely bottleneck at this point. Have you tried reaching out to NetApp? Their performance support folks are pretty good.