...of the city to stay in.  I prefer the Central Park area (I am a runner), but other's have told me to stay towards the financial district.  

It's the easiest to access via train, many different hotels to choose from and you're in the center of it all....
Since you said you're a runner and you like Central Park, you might want to be in the 50's somewhere around Fifth Avenue or Broadway as that gets you close enough to Central Park that you can do a quick jog to get over to the park and you can run the lower loop.  

....makes things a bit easier.