I would completely agree with marcussmythe's assessment on both. I've been a fan of SR when CoH first went live and stay a strong fan of it even now. If they can't hit you, everything else is mote. You can do nearly the same with Ninjutsu with a little more cost. Again, the benefit with Ninjutsu is having the Endurnce Recovery click and the Heal click for those times your Defense fails you.
Also keep in mind what your main power set is. Something that is low damage but fast recharge pairs well with SR well because then you can focus more on attacks versus extra Secondary clicks. And in there the auto Recovery. Something more powerful with slower recharge like Energy pairs well with Ninjutsu since there is the a click recovery (more immediate Endurance gain versus the lower auto Enduring recovery in SR) and heal for when you need it. Stacked with IO sets and the Fighting set you get your Resistances up with NIN while SR you can push to high Defense with some Resistance to help mitigate what small amount gets through. I'm personally still playing with Absorb effects (Practiced Brawler versus Master Brawler) but it's easy to have Practiced Brawler on Auto click and being up 100% of the time.
In the end, it's what you'll have the most fun with. SR has more toggles but less clicks. Nin as less toggles but more clicks. I like the concept of both personally. Then again I've also started chasing Energy Armor like Marcus. :p