All 3 airplanes have much greater endurance than fighters - gas delivered by a tanker is much more expensive than gas pumped on the ground; in addition, the greater weapon capacity allows a greater time on station (24 vs 3-4 JDAM max for a fighter/84 unguided MK82 vs ~28 MK82 for A-6E vs ~6-9 for a fighter). The extra sensors and crew allow better mission management for some tasks as well.
What you are not taking into account are the unique costs associated with maintaining a unique but very small fleet of aircraft with a mission that can be easily done by other aircraft. The overall costs of the B-1 are much higher than for the equivalent punch from the number of fighters, and they are much more flexible than the bombers. Stuff has got to get cut and we can't keep everything and as the redundant bomber with no unique capabilities it is low hanging fruit that deserves to get picked.