Depends on what kinda rider you are. If you like to ride like there is no tomorrow, then go for a ninja. If you like touring, going to unknown places opt for the CBR.

I am a ninja owner and i would be really honest here. THe Ninja is good in some areas but bad in others. The CBR is good in some and bad in other.

1) Revvy engine. YOu would like this Ninja screamer beyond 8K rpm. For the power to be unleashed you have to put the engine in the powerband of 8K-12K rpm. THe CBR tops out at 10K rpm but has power at lower rpms than the NInja.
2) Torque: when driving in the city the Ninja is a pain as the torque is less. On the other hand the CBR has a torquey engine and is good fun riding at lower rpms.
3) Terrain: NInja is no fun to ride on bumpy roads/offroads. THis doesnt mean that you cant take it there. THE CBR is way better than the NINja in these conditions. BUt both of them doesnt come anywhere near my bullet
4) Top Speed and Acceleration: THe NInja is better in both as it is a twin cylinder. None of them gives you a blowjob like acceleration thou.
5) Seating position: I think its more or less the same for both the bikes but i have heard mixed reactions. NOne too sporty none too upright. If you think its too sporty sit on a GT650R, if you think its too upright, sit on a bullet
6) Quality: Have had no issues with Ninja so far. Havent heard any one complaining either (except for the price of the spare parts).
7) A.S.S: THe after sales from Bajaj has been exemplary. No complaints on how they serviced my bike for the last 24K kms. Have heard that Honda has had some quality issues. But i believe they are in the process of ironing it out. See the new Ninja has been there from 2008 (the old one from 1988) and Honda from 2011. So kawasaki has had a whale of a time to iron out the issues than Honda. It might take Honda some time to resolve them fully.
8) Spare parts: Ninja is extremely costly.
Was dumb enough not to check if the side stand was on! and dropped my bike and broke the rear view mirror and had to pay 2300 bucks for a single rear view mirror. The Honda spareparts are much cheaper but there seems to be less supply since the bike is new.

So in a nut shell if you need a performance oriented, high revving bike and can take some hit on your bank balance if you drop it, go for the Ninja. On the other hand, if you are more into touring, worried about bumpy roads and lack of torque, want to go easy on your wallet go for the Honda.

Hope this helps u in making a decision.