The VII is the best U-Boat in the same way that the AK47 is the best gun.
There are better boats/guns in terms of performance. In most conditions the IX performs better than the VII.
What makes the VII and the AK47 the best is the way they have become iconic.
Ask people to draw a famous rifle and they will draw a AK47, ask them to draw a famous sub and they will draw something that looks like a VII, even if they have never heard of a VIIC. (ok, so many people will draw the Beetle's sub, but the VII will be a close second
)
That is why the VII got #1.