As much as I love Ninjutsu I would recommend Karate, especially if it's Kyokushin. Shotokan is ok.
The problem with the Bujinkan is the huge fraud base it has. This stemms from hollywood, tv, and ninja hype. Suddenly a bunch of amateurs started popping out of the woodworks claiming to teach authentic Ninjutsu when in reality they don't know jack $hit.
It is such a large problem it has ruined the reputation of the art and other martial artists will not take you seriously.
But when a good school is found it's gold. Some are better than others. Some teach all or most of the 18 skills. Most don't. The AKBAN is affiliated with the bujinkan and is very prestigious and well respected. A-lot is learned and covered including usage of firearms. Problem is such schools are few and far between.
So it's entirely up to you and what is in your area. Do you know what a mc-dojo is:
http://mcdojo-faq.tripod.com
Also if this bujinkan dojo dresses up in the costume, focus on parkour, flips, acrobatics, fake swordsmanship, or mentions "secret technique" or it doesn't have full contact sparring, etc... it's most likely a sham.
I would recommend Karate. Though there are MANY sham dojos, all about the money, and not many teach old school anymore, it's still not as bad as the bujinkan.
http://www.akban.org
If the ninjitsu is legitimate, then pursue it, but make sure you do some intensive research on any ninjitsu school you are thinking about attending. For a ninjitsu school to be legitimate it has to trace its lineage back to Grandmaster Masaaki Hatsumi. If it cannot be traced to Hatsumi and/or his 9 "approved" Bujinkan dojos in Japan, then your school is not teaching authentic ninjitsu. Like anything else, many people want to make money without having to pay franchising fees or making the sacrifice to travel and study with masters teaching the real art. Many ninjitsu organizations and schools in the West have instructors pretending to be something they're NOT because they know that "ninjitsu attracts a lot of kids who want to become ninjas."
I would choose ninjutsu. It seems very challenging.
I have 2nd kyu in karate, and I had to quit because I broke 2 bones, and it became too expensive. I want to go back into martial arts. I liked karate, but I want to learn ninjutsu. I can only do one, so I can't cross-train. Any help is appreciated. The karate was most likely shotokan.
