Like what though? Every building is a little different and the fastest way I can think of is laser cutting or CNC which is still pretty slow. Unless he was whole hog CNCing entire city blocks that is. Though the article mentions “balsa wood cut with an X-Acto knife”. If that part is true, this is utterly incredible and I have no idea how he pulled off more than 100 buildings a day.
Looking at the pictures in the article, the level of detail is not particularly great in some parts. It seems like many building have very simple shape and color. With some modeling skill, I can imagine carving and painting 100s of these in a day. Although I can't imagine doing it for 20 years.
I would however like to know what his research was like. Was he just following Google Maps/Earth? They were released in 2005 and 2001 respectively and NY has had coverage from the get go.
You don't need CNC for speed if the job is fixed and simple. You can make simple jigs and holding fixtures which firmly hold the object with features to help guide tooling. A number of these can be made to speed up all sorts of operations.