You want a hotel near the finish. Most hotels do not provide shuttles to the start. You will need to take the shuttle bus run by the race to get to the starting area. (It requires getting there early but it is all part of the experience!) The start area is a traffic nightmare, best to avoid it and ride the bus.
The race web site has a link to a service that provides accommodations. You don't need to book through them but it will give you a feel for how far away the major hotels are. There are lots of hotels in the city. You also don't need a car, you can take a bus and the T (subway) from the airport (Boston Logan) to most hotels downtown. You can also take the T to the expo and pasta dinner from just about anywhere. The pasta dinner is a great place to meet other runners but the years I went, the eating area was outside (so bundle up).
I have stayed at the Omni Parker House (can walk to the bus/shuttle and can walk back from the finish) Pretty hotel (old and historic) but regular rooms are REALLY small and only good for one person. Other than that look at Expedia or Orbitz, the distance to/from the hotel to Boston Commons will give you a feel for how far the hotel is from the shuttle buses and finish. You may be able to find a hotel to give you a ride to the shuttle bus but I wouldn't get hung up on finding one that will get you to the starting area.
