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First of all, what do you mean the "best hotel"? Best for what? What price range? With the marathon less than 2 months away, I'm not sure how much of choice you'll have at this stage.
Since the marathon starts in one place & ends in another, it depends on whether you want to be near the start or the finish. As Howard says, reservations will probably be tight by now.
reasonable area would be east side of manhattan between 59-72nd streets. This way could walk from hotel to see him run up first avenue and then walk west to central park to see him in park and then meet him at end of race.
Book asap. A few years ago my son and his college football team were playing St. John's (in Queens?), and we tried to get reservations in NYC for the night and could not b/c of the NYC marathon.