there is some differences in rubber fittings.
--there are cheap rubber fittings. and the pipes just slide into the fittings,
--then there are rubber fittings that actually have a more of "female fitting" like a sch 40 PVC fitting would have. were the pipe will only go so far into the fitting. (stops pipes from fully sliding through the fitting)
--then there is also rubber fittings that have like a "metal jacket" around them. (adds structural support to rubber fitting, to help prevent it from collapsing and/or cracking under weight, also helps from the "balloon" effect that might happen)
with above said. look for "no-hub" fittings. more likely get what you want closer than just searching for "rubber fittings".
if you get a combo of metal jacket, ends of rubber fitting only allow pipe to slide so far in, and has 2 and more likely 4 pipe clamps on it. you will end up getting something more likely to support some weight, keep pipes in place. and still allow some reduction in vibrations.
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with above said....
if you can get into the walls, ceiling, Attic, roof. and follow the actual vent pipe all the way out. see if the vent pipe is rubbing on anything. good chance when pipe was put in. that hole was not cut big enough, or pipe is leaning up against a 2x4 or like.
also check for any sort of support clamps. goto a couple local hardware stores (menards, lowes, homdepot) at least 2 of them and look at the supports they offer for pipes. (i say 2 due to 1 will have some, and the other will have the rest most likely)
there are some with springs. (attach one part to house, then a spring, and then a clamp around pipe), and then there are some more rubbish stylish clamps, along with metal pipe hangers. you may also find in the insulation isle for pipes. a roll of "wrap on rubber insulation" that you might try wrapping once or twice around pipe. before clamping a larger metal pipe hanger around pipe.
the roll of rubbish pipe insulation, might help reduce vibrations. if pipe is covered in it all the way up. but am guessing you have multiple issues with overall installations. and will need to find out were pipe is rubbing some place on the frame work of home, and re check screws that hold vent on top of water heater. and perhaps add some additional support hangers. or cut and redo some fittings. and still possibly add a rubber fitting in.
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just adding a rubber fitting in. most likely will only be a band-aid. and may not resolve issue, find the root cause.
example what happens if you can place your hand on pipe when water hater and vent kick on? does it help reduce vibration? if you slightly push/pull pipe in different directions. does noise go away?
is vibration more of an "echo" effect. errr renascence effect. (eerrr i can not remember correct word), the vent pipe acting like a trumpet, flute, etc.... and causing additional sound to be created.
