I had a quick look at availability over the Marathon weekend and it doesn't look too bad now, but I would recommend that you book asap (you can always cancel) before they announce the results of the lottery.

Is it important to you to be (relatively) near the race finish? Do you want a high-end hotel (the Ritz-Carlton for 280,000 points for a 5-night stay would be a nice splurge for a special event) or something more moderately priced?

I would stay away from Times Square because I think you'll want to minimize your exposure to stress and crowds during the race weekend. You might have a look at Courtyards around the Flatiron District or on the edge of Soho. And for a quieter splurge, there's a Ritz in Battery Park that will put you near the waterfront path along the Hudson, which makes for a nice, relaxing pre-race run.