Do both. I do. Ninjutsu (BBT) on and off for 25 years, Jeet Kune Do for less than one year and I wish I had been doing the latter far longer as it allows me to put my taijutsu in perspective against other martial arts and fighting methods, which the general closed-shop approach of most taijutsu organisations does not permit, leaving people only able to fight against other people who have studied taijutsu, because they only deal with taijutsu attacks in their kata and most of the variations.
It is easy to find someone from MMA who will permit you to break all the rules in order to spar/fight them and you will still lose.
It is easy to find an iaidoka or kendoka to test your mutodori against and you will lose.
It is easy to get into a Dog Brothers style stick fighting contest with a hanbo, jo or bo and you will lose. They will also be happy for you to break the rules but you will still lose.
But cross train in modern martial arts like JKD, BJJ and MMA, lightning fast swords styles like Katori Shinto Ryu, and full contact stickfighting styles like escrima, as well as 'ninjutsu' and you will be training according to Sun Tzu, knowing your enemy as well as you know yourself, in order to defeat them, and apparently Sun Tzu was instrumental in the creation of the ninja, so he knows what he is talking about.
Ninjutsu's/taijutsu's greatest strength is in its nastier methods, escalating the level of violence in order to prevail, usually by means of an ingenious tool or deceptive weapon, such a gun hidden in a fake sword to beat a fast draw swordsman, or shuko claws to defeat a grappler. But not only will you not be carrying any of these highly illegal items in public, but even shuko will not be much good against an MMAist if they punch your lights out or snap your arm before you get a chance to use them, plus we are regularly told that we should not hurt people if possible, even if they mean us harm, which is not easy if we have to resort to such extreme means to guarantee that we win. Which means using non-injurious grappling and striking which all these modern and sports-oriented martial artists are going to be much much much better at, because this is not only how they train ALL the time, but is also their primary objective.
Our art is a bit like having a gun but only being allowed to use it as a hammer to hit people on the toes with!