Some posts here are quite intersting. It seems that there`s still a big prejudice about being "Ninja" in western world.
First of all the word "Ninja" was actually never used until modern times. They rather used "igamono, kogamono, shinobi no mono, rappa, suppa, negoro-shu, suika-shu etc." Leaving the word "Ninja" and concentrating on these names mabye allows you to see what they really were like. Fact is not every "Ninja" was an assassin or a spy, nor was he a kind of superman. It consisted of various groups (some refugees from China/Korea, some survivors of lost wars, local people defending their region etc.), spread over the country using special knowledge about warefare and tactics. These groups fought against each other or supported each other randomly. There was a periode in Japanese history called "Nanboku" in which in particular the region in today`s Mie (former Iga/Koga/Shiga)was pretty free of government. Local buddhist sects and population had a strong feeling about freedom and did not liked to be ruled by a strong leader. Therefore there was the chance to develope more freely and that might be one reason for independent groups (mentioned above. You would call them "Ninja").
Also samurai before 16th century were not so much in all the stuff you know about Bushido. There were almoust 100 years of war, and how are wars won... by cheating! Think of Oda Nobunaga who used guns. It was quite common to use guns in battle these times!!! It is hard to say what people really did, but with Edo jidai (Beginning 16th century) our all image about bushi/samurai started. So you can`t really divide a "ninja" is supposed to train just that school and nothing more. Rather training a live long, they applied (They had no 30 years to learn!!!). If they were not skilled they simply died

(What was acctually the same for most of the Bushi, of whom some of them were "Ninja").
Speaking about Bujinkan and the schools, which are "true Ninja" ryuha and which would be not: well Gyokko ryu (which is supposed to be a "chinese school and therefore not ninjustu" (Berador wrote that)was the basic of many other schools (even supposed "Ninjutsu" schools). People did not just train one particular school, and calling something Chinese or Japanese doesn`t really make sense, because there was simply an exchange of knowledge. In fact even in China and Korea they had people spying and assassinating, secret societies. And if you leave the word "Ninja" away it becomes the same like in Japan.
You can easily compare that attitude to Toda sensei, who thought various schools and was sword instructor at the Koubusho. Therefore he had to be Bushi (but wait, he also was Soke of Togakure ryu). He finally inherited them to Takamatsu sensei who gathered and learnt new schools until we finally reached our today`s 9 schools in Bujinkan.That is not something new, but a habit as old as humans are.
So what makes you to be a "ninja"?

In Bujinkan (when you have a good teacher) you have a good chance in learning some points.It is not just the physical confrontation, endless repetition of all the single waza and the skill to fight. Rather then winning a fight, be concerned about not to loose a fight. Social skills, psychology, knowing yourself (body and limits) and your environnment is pretty essential.
If you like to see modern practicing "Ninja" have a close watch on the CIA, which originally learnt from the Japanese intelligent service ("Ninja"), which was called Nakano gakko. And then listen to Hatsumi sensei and it becomes obvious what he is acctually doing for so long time.
So forget about movies etc., if you are interested how they used to be.