I know your post was over a month ago, but I was wondering if you're still looking at SAN vs. NAS performance on your NetApp system.
I would definitely recommend running representative workloads on both datastores and then looking at perfstat output from your NetApp system.
Can you give me a more detailed description of your NetApp filers? How are they connected on the NAS side (e.g. 1 GbE vs. 10 GbE)? Do you have Flash caches in your controllers?