Wow can't believe I missed this one. I spent a good few years in Muay Thai, and am now training in the Bujinkan. I'd say personally that yeah you can learn a lot of good stuff from Muay Thai, some of which may or may not work in a given situation out on the street.
I have successfully used what I learned in Muay Thai to defend myself, and have also tried on other occassions but ended up getting my rear end handed to me...
As for what I have learned in the Bujinkan, well. To quote a certain janitor from MadTV: That took it to the HNL. Hole Nuvva Level...
Yeah it's a different approach, different purpose, different philosophy. But honestly I keep hearing people on the net trash talk ninjutsu but seriously the stuff I have been learning, particularly the psychological aspects and intent aspects, has literally helped me to simply "not be there" in a confrontation, rather than hanging around and having to punch it out.
I have also used it to neutralise a few particularly vicious attacks, whilst remaining clearly a law abiding citizen in my actions, and on one occasion disarm somebody who was suicidal/self harm-ish, wielding a knife and threatening me.
All said and done you need to find the path that works the best for you, and make your journey for we are all pilgrims here, friend.
My .02 though is that Muay Thai has certain limitations in being sport based, however you can work around these if you really intend to, and also the two gyms I trained in the philosophy was pretty much smash the f@#k out of the other guy til he drops or it ends somehow.
Ninjutsu, I believe, is more of an art of "subtle diplomacy" so to speak. In fact I remember being taught that even when the ***** hits the fan the object is to reach a "point of negotiation" so to speak!