In

"In." Part of the explanation from a book called "The Grammar Answer Key," by Keith S. Folse, is: "More specific places use 'at,' while large places tend to use 'in.' 'On' is for streets (or similar words such as 'avenues' or 'highways.'" Folse adds four specific cases: For an address with a house number use "at:" "I live at 2251 Walnut Street." For the name of business or similar, use "at." For a street (or similar), use "on." For a city, a state, a province, a country, a neighborhood, use "in." Apply this to a trip I took last weekend, we went to see the total eclipse of the sun, and we viewed the eclipse IN Burlington, Vermont, where we stayed AT the Best Western Windjammer Inn ON Williston Road.

'How long did you stay in New York?' is correct.

We usually stay ‘in’ a city. But there are certainly circumstances where ‘New York’ can work with ‘at’ because ‘New York’ takes on a different meaning. Taylor Swift gave a great concert at New York. (=at the stadium in New York where she played) Customs is slow at New York. (=at the airport in New York.) Whenever I have a long layover I get a hotel room. I stayed at New York for 12 hours last week. (=at a hotel near a New York airport)