Is there any reference which confirms that Meruem is much more powerful than Hisoka? In the Hunter X Hunter anime, Meruem is said to be (arguably) the strongest character in the series. However while reading about Hisoka, I found that he once thought to challenge Ging to a battle to death, which seems astonishing because Netero once said that Ging is one of the five best Nen users in the world. 

Is there any reference (either in the manga or in the anime) that conclusively says that Meruem is far more powerful than Hisoka?

Note: In the anime, Neferpitou's aura is reported to have much more murderous intent that both Hisoka and Illumi's, but I don't know whether it necessarily implies that Hisoka is weaker than Meruem.
Meruem is actually the strongest living being in term of Nen Aura. This is also due to his Nen consumption ability, as seen in his wiki article:


  Meruem's initial ability gives him strength through consumption.
  Meruem's aura grows every time he devours a user of Nen, with their
  aura synthesizing to his own.


Additionally, Netero, who was one of the strongest characters in Hunter X Hunter, couldn't really beat Meruem. Don't forget what he said to Meruem when he met him:


  When? When did I start waiting for my opponent to make the first move?
  When, indeed? It became a routine. The loser held out his hands in
  gratitude for the lesson and I graciously accepted without skipping a
  beat. As if that was what I wanted!! That's not how it should be!! For
  so long, I sought the height of perfection. I dreamed of giving my
  heart and soul to battle an unstoppable adversary!! I'm a lucky man.
  I'm thankful for everything that led me to this point...that led me to
  you!!


So considering this, Hisoka has to be weaker than Netero, who is indeed weaker than Meruem.

But as already said in Kalilz's answer:


  When it comes to a fight between Nen users, pure power doesn't mean everything. One may have an ability than can overpower a type of opponent.