Are pull-ups the best upper body exercise?
Like all things fitness-related, the answer to this question is: it depends.
The pull-up (and all variations of grip, bar and width) is a fantastic upper body exercise, and when it comes to maximal muscle stimulation it's definitely up there. Not only are you activating the muscles of your upper, mid back and arms, when you do them correctly, you can also get a significant core and hip flexor activation to boot. Additionally, the pull-up can be a great movement to help increase shoulder range of motion and flexibility.
Now, if these are all the benefits, why do say "it depends?" Well, it's very simple, the necessity of the benefits provided by the pull-up are all predicated upon one's goals as well as one's ability to perform the movement.
Given the large number of muscles activated in the movement, the pull-up can actually be a sub-optimal movement when looking for pure back development. In many cases, the biceps and grip become a limiting factor, and the fixed nature of the bar (assuming you aren't using rings) can put significant strain on the shoulder when performed with very high volume/frequency.
If back hypertrophy is a primary goal, you might be better served by performing dumbbell and barbell rowing movements with straps to take the grip out of the equation and focus all of your attention on your back muscles.
Additionally, if you're a competitive powerlifter or Olympic weightlifter, there's little benefit to your competitive lifts by doing a pull-up aside from off-season training protocols.
At the end of the day, I think pull-ups should be included in all training programs, as primary or assistance exercises, but they should be considered as a part of the whole program. Look at the other muscles of the back and arms, and other exercises that may work those muscles better.