Why not - lots of people do. Actually it's common shorthand and quite useful when parties to a conversation know which city is being discussed. Depending on the conversation it also gets called the Apple, City that never sleeps, NY, NYC, Noo Yawk, Times Square, etc. If I say I'm flying into LaGuardia or taking the train to Penn Station most people will know I'm going to New York City without me saying so. Context is everything when understanding a conversation.
Also, take a look at S.F., San Fran, Frisco, or the City by the Bay for an example of where not to build a city.
But many of our cities were built in locations that had we known more at the time we would not have chosen that site. For example I lived not far from an oceanside peninsula that was first developed in the late 1940's with houses. Those lovely houses were fine until we got a multi-day rainstorm that percolated down to some old clay strata that sloped downward towards the sea. The houses began slowly sliding downhill and over the cliffs. Those houses were built before we knew enough to conduct geological surveys that would have revealed the remains of an old mountain that included many sedimentary layers.
