Ninja were essentially hired assassins and guerrilla fighters, and as such a core art of ninjutsu is stealth. The word Ninjutsu (忍術) itself translates as "the art of stealth." A lot of their fighting forms and weaponry look similar to what the Samurai used... I don't know how many of those forms are actually exclusive or unique to Ninjutsu. I've never come across a school that teaches Samurai/Ninja Taijutsu, but Jujutsu and Aikido are descendant from Taijutsu (that's why the Aikido uniform wears the Hakama at higher levels, and they practice fighting in Seiza sitting position -- Aikido also favours broad sweeping movements, similar to the way you'd swing a sword). Kenjutsu, Bojutsu, Sojutsu, Naginatajutsu etc. are all taught as separate styles.
I think one massive problem you're going to come across if you want to learn Ninjutsu is trying to verify authenticity. Trying to find an authentic school in
any martial art can be a challenge, but Ninjutsu might be even more challenging because the art was heavily shrouded in secrecy. There's a historian by the name of
Stephen Turnbull who's done a lot of excellent research into feudal Japanese military history (he lived in and travelled extensively around Japan for several years while doing his research). You might like to check out his book
"Ninja: The True Story of Japan's Secret Warrior Cult".