The ninjas past is covered with quite a bit of secrecy, according to Wikipedia (not always the best source of reliable info!) the earliest recording was written in the 15th century. They were used for selective strikes, espionage, assassination, and infiltration of enemy strongholds.
The actual look of the ninja is a bit unclear. Some believe that they original wore suits of armour similar to that of the samurai's. Ninja's probably didn't wear all black as commonly associated. In the old Japanese Kabuki theaters actors portraying ninjas would wear black costumes to give the audience the impression of being invisible but a real ninja would have probably worn colours similar to the environment he/she was around, to blend in easily. Apparently dark blues, even reds were more effective at night than black for invisibility!
That's the insulting history lesson over, I'm sure if any real ninja are alerted to this I'll have a shuriken coming this way real soon!
So how did ninjas get into the pop culture of today? Although they have been depicted in many books over the years (I'm sure) and in the last century in Japanese films, it was probably the 1967 James Bond film, 'You Only Live Twice' that really introduced ninjas to the majority of the world. They were used as deadly assassin's but not too deadly since James Bond had to inevitably kick their asses being the lead.
America in the eighties saw a huge boom of ninja on screen, often with Sho Kosugi donning the black costume in various roles. Used as cannon fodder, wave upon wave of ninja would appear in these movies, solely for the purpose of being killed easily by the main American actor. Lets not forget the crossover, 'American Ninja'. This film marked the moment it was actually kinda cool to be a Ninja and introduced the idea you didn't have to be Asian to become one.
Believe it or not, Lee Van Cleef (from 'The Good, The Bad and The Ugly') played the lead ninja in the TV show 'The Master' back in the eighties.I'm not going to pretend that these films were any good. Although I get my own enjoyment watching them I class them as cheap, bargain bucket throwaway films. They were so bad they became funny. Its a combination of terrible scripts, cheesy acting, crap stunts and poor funding that does it for me.
Once it gets to a comedy level it then becomes easily accessible for children. Dumb down the violence a bit and its perfect for kids to enjoy. 'Teenage Mutant Ninja Turtles' (one of the most ridiculous concepts ever although one I got fully absorbed into as a kid) was a really popular franchise and I'll assume the '3 Ninjas' films were too although I won't admit to watching any of them.
In answer to my original question, "When did Ninja's become funny?" I'd have to say it was the eighties although it was probably unintentional.