The Inn at Harvard Square is the closest hotel to Harvard Yard (diagonally across the street); the Sheraton Commander and Charles are both slightly further but still only a 5-minute walk. The Doubletree that Pickles mentions is indeed near the Business school, but it's in an entirely different city than where you'll find Harvard Yard. (Ok, so it's just across the river, but still a 10- or 15-minute walk. And that Doubletree is 100% useless if you don't have a car.)

The place that might be the most interest to you is the relatively new Residence Inn (part of the Marriott chain) near Kendall Square. All the rooms include kitchen facilities. It's is not within walking distance of Harvard (though it would be a pleasant walk if you had the time and the weather is nice), but the hotel is just a few minute's walk from the Kendall subway station, 2 stops from Harvard Sq.