I've used and deployed both of those, and I would say they are fairly equal. Northern are very responsive to the community and we've had a lot of input in to what we wanted to see from the product, so they are keen to keep users happy! NTP QFS is possibly a more mature product in relation the NetApp integration, and they probably have a larger install base.
Not sure if I have a personal preference between the 2, they are fairly evenly matched and both have their benefits. Have you applied for eval copies? Great way to test is with soft quota's. The biggest limitation always is with file ownership. A users quota has to be powered by the filer ownerships, and often "Administrator" owns a fair proportion of files. This is something you might want to look at fixing first as all software packages suffer from this limitation.
What functionality are you looking for above what NetApp native quota's offer?