The S-300 and S-400 (SA-20 and SA-21) family of long-range SAM batteries are the best area denial air defense system Russia has ever built and exported, matching or even marginally surpassing the latest Patriots.
S-400 (SA-21 Growler)
PAC-3 Patriot
I doubt the Israeli Air Force will ever be able to eliminate the Iranian nuke facilities unless it occurs prior to the SA-20 deployment in Iran, and the batteries could be possibly operated by IRIAF missile crews under Russian supervision.
Hate to break out the bad news, but the SA-20 deployment would give the Iranian IADS a huge boost in air defense capability, unifying the land and ship-based SAM and AAA batteries, along with radars and jet fighters under the IADS umbrella.
Israel could do it using ICBMs with with nuclear or tungsten warheads. A follow up raid by 100 F-16Is and 25 F-15Is escorted by 40+ F-15Cs would be nice.