A sonic boom is percieved by an individual (or your windows) as shock waves pass over you that are generated by the airframe of an aircraft transitioning or flying faster than the speed of sound . (Yes, that's a very non-technical explaination.) These shock waves are a function of moving through the air. There is no connection or relationship to the ground, other than a separate measurement as to how fast you are passing by the ground. We make multiple measurements of speed in an aircraft. In this case, Mach is your speed relative to the speed of sound. The airliner you sit in might be doing mach .81, which is 81% the speed of sound at that altitude. Fighter aircraft might accelerate to mach 1.5, which is 1.5 times the speed of sound at their altitude. At the same time, those aircraft are measuring their True Airspeed (tas), Indicated Airspeed (ias), Ground Speed (gs) along with other variations such as Calibrated Airspeed (cas).
Everything the airplane is experiencing is in relation to the "body" or in the case of the jetstream for our purposes here, the "river" of air it is passing through. Drag, friction with its associated heat rise, lift, ability to make thrust.
If you fly east through the core of the jetstream, you may be in a "river" of air moving east at, say, 100 knots. If your true airspeed is 450 knots, then when you add the 100 knots of the jetstream, you have a speed over the ground or ground speed of 550 knots. Do a 180 degree turn and go the opposite direction west through that same jetstream. You have the same true airspeed of 450 knots. You also have the same body of air in which you are flying moving the opposite direction, east, at 100 knots. 450-100 gives you a ground speed of 350 knots. You are flying at 450 knots, but moving across the ground towards your destination at 350 knots. This is why airline flight times west-bound are generally higher than east-bound times, especially in the winter when jetstream speeds are significantly higher.
As you fly back and forth across the country at 450 knots in this hypothetical, you also read your mach number, which is, just for example, mach .78, or 78% the speed of sound. At this mach, the airframe is generating various shock waves. These shock waves are not generating the "boom" that reaches the ground as in a supersonic aircraft. These shock waves are not affected by the jetstream being on our tail and increasing the ground speed or the jetstream being on our nose and decreasing the ground speed. The shock waves remain the same because we are flying through a body of air at .78 mach. The ground speed is irrelevent. A huge tailwind in the jetstream will create a fantastic groundspeed, but it will not create a sonic boom because the airframe is "only" making the shock waves that result from a mach of .78.
As was previously stated, a canoe being paddled at 2 mph downstream in a river flowing at 2 mph is going to pass the bank of the river at 4 mph. Turn the canoe around, paddle at 2 mph and you have zero relative movement to the bank in a river flowing at 2 mph. Increase your paddling to 3 mph and you begin to pass the bank at 1 mph. Same concepts, one is water, one is air.
