The title is a reference to the song "Moon River," which is from the film. The song is also played during the credits, which was also dedicated to Andy Williams who died of bladder cancer on September 25, 2012.
In two scenes, Mary is dressed as Holly Golightly:
In one, she is wearing the same black dress and hat with the white ribbon around the hat.
While playing guitar, Mary is dressed similarly to Holly while she plays guitar, albeit with a red bandanna as opposed to Holly's white.
In the film, Holly left her "family" to set up a new life in New York, much like Mary does here, though her dad comes to get her, not her husband like in the film.
Fievel Mousekewitz, the main protagonist of the 1986 film An American Tail is mentioned by Homer who thought that Fievel was his ancestor.
The September 11 attacks was touched upon slightly when Bart tells Homer that he "would love New York, now that [his] two least favorite buildings have been obliterated." Bart then quickly adds "Old Penn Station and Shea Stadium," after a pause.
George Tooker’s painting Subway (scene when Bart and Homer enter the subway).