According to the Jonathan Songfacts, the song was inspired by the kindness Apple's former boyfriend Jonathan Ames showed her during a trip to Coney Island.
APPLE: I did that because Jonathan likes his name to be spoken. He pisses me off in so many ways, but I’m still very close with him. I felt like he deserves to have a song with his name in it. I was staying in an apartment in New York and he was just starting up…
Jonathan, call again
Take me to Coney Island
Take me on the train
Kiss me while I calculate