I prefer walking in the city.
Even though buses and the subway are convenient, I end up walking everywhere. It seems there is a story, picture, or drama playing out right in front of your eyes at every street corner (rarely it's the kind of drama you were not looking for). It always amazes me how much New York has changed since 1980. What was then very gritty at best, is today safe and friendly, but not in a coiffed way. When I traverse the city I usually stop at some coffee staples, such as Via Quadronno, or La Maison du Chocolat. A truffle and espresso provide fuel for maybe 2 hours, although long museum/gallery visits call for several pit stops during the day. The good thing is that there are so many great places anywhere in the city, and you never have to go far. In the summer, it is hard to beat a rooftop bar with spectacular views, the 230 Fifth. http://www.230-fifth.com/ I'm skipping restaurants for now, as there are too many to mention.