During production of Star Wars: The Force Awakens, J.J. Abrams was considering including the skeleton of Jar Jar Binks as a hidden easter egg, but he ultimately decided against it. Jar Jar was perhaps the most despised part of the prequel trilogy, so showing his dead body would have let everyone know that Abrams is going back to the atmosphere of the original trilogy while leaving the prequels behind.
Though we did not see Jar Jar's skeleton, that doesn't mean that he wasn't killed during the events of The Force Awakens.
Warning: This theory discusses spoilers for Star Wars: The Force Awakens, read at your own risk.
Similarly to the Death Star's destruction of the planet Alderaan, [Star Wars: Episode VII — The Force Awakens](tag:711158) showed us the First Order making use of their new super-weapon, Starkiller Base. Instead of just destroying one planet, Starkiller Base harvests the energy of the sun to destroy many planets at once.
When General Hux fired the weapon in the second act of the movie, we saw its blast spread apart to obliterate several planets, one of which looked rather familiar to us. In fact, the planet that they focused on showing us the most in that scene was the planet Coruscant, which was a major part of the story for episodes one, two, and three.
In the prequel trilogy, we saw that Coruscant was home to two major buildings. The first of which was the Jedi Temple. Though many archives and monuments may have been destroyed there, the building was most likely vacant, due to the near-extinction of the Jedi Order.
However, the second building wasn't vacant at all. In fact, it housed thousands of different life forms from hundreds of different planets. That's right, I'm talking about the Senate. While you all may have hated all of the political jargon during the senate meetings in the prequel trilogy, it still included delegates from all over the world, including one particular Gungan from Naboo.
That's right, since Attack of the Clones, Jar Jar Binks has been a member of the senate as a delegate from Naboo. That could mean that he was likely on Coruscant when it was obliterated.
Of course there are several factors which could determine if he was present on the planet. Maybe he wasn't on Coruscant at all. Maybe he was safely underwater in Naboo. That still doesn't mean he was safe.
The Starkiller Base didn't just target Coruscant. It targeted the entire Republic, as we learn from the meetings of the Resistance. Unfortunately for Jar Jar, Naboo was a major member of the Republic. In fact, the entire plot of The Phantom Menace was Naboo trying to fight fact against the Trade Federation. When Padme became senator of Naboo, she was one of the most outspoken voices of the Republic.
Even though The Force Awakens takes place decades after the prequel trilogy, it is still very likely that Naboo is a part of the Republic. That means unless he decided to go on vacation to Tatooine, Jar Jar is likely deceased now. Well done J.J., it seems like you didn't have to include his skeleton after all. All you had to do was blow up his planet.
Update: I've been recently notified that the planet that was destroyed in The Force Awakens was actually Hosnian Prime, not Coruscant. However, it was still the home of the Republic, so it is likely that if the Republic was re-located to the Hosnian system, the senate could have been moved there as well. If Jar Jar is still a representative of Naboo, he could have been on Hosnian Prime as well.