I honestly think that Heatran is by far the best counter to Jirachi. Other than the rare SupeRachi carrying Hidden power ground, it counters every set.
Heatran takes abysmal damage from both Iron head and Body slam. The only other offensive move that standard Jirachi uses is fire punch, which even gives Heatran a flash fire boost. Heatran can relatiate with Lava plume/Fire blast (depending on the set that you're running) or earth power.
Calcs:
As you can see, Heatran pretty much screws Jirachi over.