Great:
Royal Sonesta Hotel over in Cambridge, just across the bridge. Good access to the T, no keys on the elevators (they have two towers, so different banks of elevators.) and you can completely ignore the front desk.
Marriott Copley
Omni Parker House Hotel - Small rooms, but very nice
Hilton Boston Downtown (on Broad St.) -Huge room, really loved it. A bit of a walk to the nearest T however they do have valet parking.
Westin  

Avoid  
Le Meridiene in Cambridge. Great Location in terms of shopping and restaurants but the elevators are directly in front of the desk and require keys at all hours.
Waltham hotels have great rates, however they aren't very conveniant. I stayed in the Westin once, and while I loved it, it was a $75 cab fare from downtown.

How about the Presidential suite at the Ritz-Carlton Boston Common? Only $6,000 per night.

But seriously, something a little more specific in price range would make it much easier to give suggestions.

-- Modified on 6/23/2013 4:26:35 PM

Royal Sonesta is nice. There is also a hotel across the street, I forget the name. It is nice as well.
Marriott LongWharf is a fav but I am a Marriott guy. Good views and near Faniel Hall.

Naming specific hotels and their policies on a public board is not in the best interest of the community, IMHO