I put in new furnice and water heater.
Should I remove my unused chimney before I replace roof
Anytime you can remove a hole in the roof is a good thing.
If your chimney is not used after you replaced the furnace and water heater and you want to remove it, go ahead. Just don't wait forever to replace the roof.
Start ripping that chimney down from the top and repair the roof soon after you drop the brick layer down below the roof's framing. Otherwise, you will need to get a massive tarp that covers over the roof ridge and well beyond the opening of the chimney opening.
My chimney tear down took about 3 or 4 days.