As for hotels, I've had AWESOME luck with Priceline.
On 3 seperate occasions I've asked for a hotel in the Boston area, and included Cambridge by the river. I then set my price at $80, and I've gotten the Hyatt Regency EVERYTIME. Now, since this is Priceline, I can't guarantee anything, but it hasn't failed me yet.
Here is the hotel:
http://cambridge.hyatt.com/hyatt/hotels/index.jspFrom the picture you may recognize the hotel from trips into the city.
Its right on the river, but on the Cambridge side. They also have a shuttle that will bring you to Harvard Square or Kendall Square (T Stops). From there you can go where you need to.
Also, if you do select this, and get a room. You can then call up the hotel directly and ask for specific rooms. Certain rooms have a great balcony.
I've done this everytime too, and it hasn't failed. They've always been incredibly accomadating.
I would avoid the Double Tree mentioned by Goonz. Its too outside the city for a weekend in the city IMO. Also, its not really close to BC either, not that you want to stay that far out.
