Either right in Boston (MA) or outside - up to about 50 miles out. IF
it turns out there are lots of choices, I'm most interested in places
right along the coast. I know hotels around here can be very pricy,
but I'd prefer something less than $200. No preference for hotels over
motels.

According to this site, 
http://www.bnbboston.com/boston-bnbs/b&bs_4a.htm
  
Kingdom Fine Arts B&B has a room with a waterbed:
  
"The 3rd floor offers a 2-bedroom (one with a bed with a regular queen
mattress on a waterbed plus a single cot and one with a king bed and a
queen futon sleep sofa), 2-bath apartment with full kitchen and formal
dining room."
 
Here's their website: 
  
http://www.kfabb.com/