In reality, there's a lot of overlap between ninjitsu, aikido, jujitsu, and karate.
There's a lot of differences. It's not a simple question to answer. Many of the jujitsu schools, karate schools, and aikido, of course is gendai budo, which are some of the newer martial arts schools in Japan, and don't focus quite as much on some of the traditional elements that are covered in many of the kobudo older schools.
That could be one important distinction between many of these newer karate, jujitsu, and aikido schools and the more traditional old schools is just the difference in the types of weapons and some of the techniques that have been refined and specialized within the modern schools of martial arts.
That's just a little bit about the difference between ninjitsu as it relates to kobudo and karate, aikido, and jujitsu as it relates to gendai budo or the modern martial arts schools.