I've never been to San Fransisco, but I heard that is it very clean. I practically live right around the corner from NYC, and I have to say that I never ever get bored of that city. I've traveled over seas and up and down the East coast, and I still have not seen a city that matches the vibrancy of NYC. Everything is at your fingertips regardless of your tastes. The city isn't as dirty as some people may think. One other poster stated that it isn't as seedy as it used to be. That's true. The subways are actually cleaner and safer than they used to be. In fact, they are in the process of installing new state of the art subway trains.
On the flip side there are certain areas that are dangerous, but if you're smart and alert you should be fine. I believe NY is the safest big city in the country. It is a very fast paced city, and the people probably aren't as friendly as the people from San Fransisco. Also, during the holiday season the city becomes claustrophobic between the tourists and holiday shoppers. San Fransisco has the edge in weather, although our past couple of winters have been mild. The summer can be brutally hot.
Since NYC is in the Northeast you also have Boston, Philadelphia, and Washington D.C. just a few hours apart from each other.
I'm sure San Fran. is a beautiful city, but don't forget about the potential for earthquakes. Then again, forecasters have said that NYC is due for a hurricane, so take your pick.