What term can I use to express the delay between two connecting flights?

layover

is the term for the wait between the arrival time at an airport (not the final destination) and the time of departure.

In American English, this is often called a layover,

a short stay somewhere between two parts of a journey

In my experience, it is most commonly used to describe a wait of several hours between flights or trains, during which you often do not or cannot leave the transit hub. How long is your layover in NYC? Can we meet for lunch?

Layover is sometimes used to describe an overnight stay, but in American English I would tend to ask, instead, How long are you staying? if I expected the answer to be that you were staying at least one night.