Thump the flue pipe, you might alter the angle or how its fitted its only got a little mm gab between pipe and what its resting against that is making the rattle sound, try thumping it may cure the issue.
Also heat expands and cold makes items shrink inwards so weather is gonna be a factor all year with changing things such as windows or doors that can even rattle with low sub bass tones.
One way check for resonance is using a sine wave frequency sweep ether a quick sweep or manual sweep one Hz at a time and at various volume fader levels SPL db of each and all speakers to see if you can detect an resonate noises in or around the home.
Don't play it at levels where its gonna do damage to the speakers care should be taken when doing this that you don't harm your hearing as some frequencies in your room will peak high and lesser in other areas of the room.
Free sine wave generator is level 1 It has basic 1/1 octave RTA/sound generator and oscilloscope ( use the 1/3 octave version that you have to pay for)
https://www.trueaudio.com/rta_down.htm
Also there is free REW that even comes with a kitchen sink fitted and the sound generator on its what I must use.
http://www.roomeqwizard.com/