Ever hear of shaped charge warheads?
There's been a lot of R&D into this area concerning nuclear devices. Even if the bunker facilities are buried too deep to be destroyed outright, a hit close to the access tunnels would turn the underground labs into tombs for the people working in them. Either way, mission accomplished.
I'd much rather deal with the fallout of 2 or 3 nuke bunker busters than I would from the massive retaliatory strike Israel would launch should Iran's President make good on his threats to wipe them from the face of the Earth.