Part of Magruder's Curiosity Cabinet is set on Hoffman Island, a real place in Lower New York Bay where sick immigrants to the United States were quarantined in the early 20th century. The characters also discuss Swinburne Island, a smaller island near Hoffman.
Source: Flikr user jag9889.
Many people don't realize that there are actually a large number of tiny islands all around New York City. Some, like Hoffman and Swinburne are man-made. Here is some very cool drone footage of one of those islands--it's not one of ones discussed in the book, but it's similar.