Make sure you need a new boot - may just need a bit of bitumastic caulk if it is leaking a bit at the duct contact, as they commonly do as the rubber gets older. If split, then yes it needs replacing though a good wrap with waterproof duct tape or bitumastic caulk will keep it intact and dry until a roofer can fix it.
Cost depends on the type - if type with replaceable boots, about $40 each in labor, ballpark. If not replaceable or can't get the replacement boots, then the entire roof jack (the sheet metal cone with the boot and flat metal base) has to be replaced, which means it has to be pulled out from under the overlying shingles and off the duct that connects through it, and typically that means removing about a 3-5 foot area of shingles because commonly you cannot pull the duct out easily to allow you to slide the jack out from under the shingles. Therefore, the better part of an hour per unit - so more like $50-80 labor per.
There will probably also be about a $10-40/unit materials cost depending on whether the entire roof jack has to be replaced, and a minimum labor charge on the job of probably about $100 if you have only one to do.
There is another alternative which does not look as pretty but works, depending on the configuration and size of your jack - is to pull a new boot, or boot and part or all of the cone from a new jack, down over the existing with bitumastic caulking applied first, as an over-boot, if you will. This fits the new boot around the vent pipe properly, just a bit higher than the old one, and the new boot and piece of jack acts as a skirt over the old one, and can be pop riveted on to keep it from lifting off in wind. This means the $40 or so per jack replacement cost, but cuts your labor to probably about $20-30/unit, and also totally avoids disturbing your shingles - a big bonus, as every time you mess with them you introduce the possibility of introducing leakage.
if the boot you are taliking about is covered with a vent hood, like for a kitchen or bathroom vent - then the higher end of above cost, as the hood has to come off before the boot can be worked on.
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