Compute the probable volume of the underground complex...
Compute the amount of air the hundreds or thousands of workers require to survive...
Seal all surface accesses to the underground facility, leaving redesigned accesses that would allow either air evacuation or poison gas injection...
Destroy all water and power entry points on the surface...
Sit back and wait...
Use swarms of drones to drop ordinance on all surface accesses to the underground facility to plug them shut. However, are any humans even in there right now or is it temporarily shut down?
Thus, the bunker buster bomb is probably the best way to destroy the actual underground facility, rendering it useless for years to come, probably forever. Do it Prez Trump, act decisively and do it now before Iran can come up with a scheme of their own.