It sounds expensive ! I wonder why none of the builders / roofers offered any alternatives as you are using a back boiler ?! I would ask if that is the only way forward - as obviously this has a knock on effect on your boiler too !
If it's still in use with the boiler it cannot just be removed. If you definitely need to remove it - You could retain the boiler & fire and get the chimney repaired/removed OR You could get a new combo boiler sited elsewhere with new wall flue and remove the chimney. OR you could replace the boiler and rebuild the chimney and get a new fireplace fitted. But does it definitely need removing - Why is the chimney leaking? Does it require repointing, reflashing or does it just need a little rain hat - chimney cowl? Which would be the most common repairs to a leaking chimney. If they are recommending removal has the condition of the chimney deteriorated so much it could be leaking fumes into your house from the boiler? If so this is urgent.