Do bigger aircraft make a bigger sonic boom?
The short version is that yes, larger aircraft create bigger sonic booms, but you still have to be flying very low (less than 100 ft.) and really trying hard in order to damage glass.

A sonic boom is so complicated that you will not find a simple formula to determine the strength.  This article describes a modeling tool called PCBoom3 which can be used for sonic boom calculations.



According to several different sites, like this one and this one, the size of the aircraft does affect the intensity:


  Factors Affecting Sonic Boom Intensity
  
  The intensity of sonic booms are affected by:
  
  
  Weight, size and shape of the aircraft.
  Altitude
  Attitude—orientation of the aircraft’s axes relative to the its direction of motion.
  Flight path.
  Atmospheric and weather conditions.
  
  
  As the size and weight of the aircraft increases, the intensity of the
  sonic increases. This is because a larger aircraft displaces more air,
  and a heavier aircraft needs a greater force of lift to sustain
  flight. Thus creating a louder and stronger sonic boom.


and


  General Factors Associated With Sonic Booms
  
  There are several factors
  that can influence sonic booms -- weight, size, and shape of the
  aircraft or vehicle, plus its altitude, attitude and flight path, and
  weather or atmospheric conditions.
  
  A larger and heavier aircraft must displace more air and create more
  lift to sustain flight, compared with small, light aircraft.
  Therefore, they will create sonic booms stronger and louder than those
  of smaller, lighter aircraft. The larger and heavier the aircraft, the
  stronger the shock waves will be.


NASA says that a typical sonic boom for the F/A-18 is about 1.4 psf and a different NASA page goes on to say:


  Overpressure Sonic booms are measured in pounds per square foot of
  overpressure. This is the amount of the increase over the normal
  atmospheric pressure which surrounds us (2,116 psf/14.7 psi).  At one
  pound overpressure, no damage to structures would be expected.
  Overpressures of 1 to 2 pounds are produced by supersonic aircraft
  flying at normal operating altitudes. Some public reaction could be
  expected between 1.5 and 2 lb.  Rare minor damage may occur with 2 to
  5 lb overpressure.
  
  As overpressure increases, the likelihood of structural damage and
  stronger public reaction also increases. Tests, however, have shown
  that structures in good condition have been undamaged by overpressures
  of up to 11 lb.  Sonic booms produced by aircraft flying supersonic at
  altitudes of less than 100 feet, creating between 20 and 144 lb
  overpressure, have been experienced by humans without injury.
  
  Damage to eardrums can be expected when overpressures reach 720 lb.
  Overpressures of 2160 lb would have to be generated to produce lung
  damage.
  
  Typical overpressure of aircraft types are:
  
  
  SR-71: 0.9 lb, speed of Mach 3, 80,000 feet
  Concorde SST: 1.94 lb, speed of Mach 2, 52,000 feet
  F-104: 0.8 lb, speed of Mach 1.93, 48,000 feet
  Space Shuttle: 1.25 lb, speed of Mach 1.5, 60,000 feet, landing approach
  


They also include a graphic that shows the difference in sonic boom between the F-18 and the Concorde, with the Concorde having a much greater sonic boom at the same alittude:





This article specifically covers glass:


  Glass. Poorly mounted, undamaged glass in the greenhouse was chipped
  by impact against nail holding points at a sonic boom overpressure of
  12.1 psf. The same type of glass, which was already damaged, was further damaged at a designed overpressure of 7.9 psf. A large
  one-ninth of an inch thick window, intentionally precracked from
  corner to corner, was further damaged by booms of an average 6.5 psf
  overpressure.


So typical sonic booms generated by normal aircraft aren't going to create anywhere close to the 12.1 psf that they say is needed to chip "poorly mounted" glass, but the strongest sonic booms can get well over this.