The three options include using a special forces team, in which case a Sayeret force would be inserted and tasked with destroying the facility. Obviously that would be a one-way mission for the team, but considering what is at stake Israel would not be in any way short of capable volunteers. The ability of this succeeding though is not that high.
The second option is a nuclear strike. Israel can simply launch a number of its Jericho missiles at the site. Their yield would be sufficient to level the facility, and more importantly get to the underground facilities. The Jerichi nuclear MRBM has the three things I mentioned - range (can get to Iran with no problem), payload (a nuclear package will definitely do the job), and survivability (not many nations can intercept an MRB). However, the chances of Israel opting for a preemptive nuclear strike is the same as that of Clint Eastwood sending Obama a Christmas greeting card. Simply not going to happen.
The third option is a major cyber attack similar to that which crippled the Iranian nuclear project for a while (and that which crippled the Syrian air-defense network). It has worked before. The only problem here is that the Iranians are many things, but stupid is not one of them. If the Persians were to dedicate themselves to better things rather than fulfilling the wetdreams of the Ayatollahs Iran would be quite far. They obviously know what Western cyber attacks are capable of, and anything that is vulnerable has definitely been taken off grid. The only way a cyber attack would be possible is through HUMINT sabotage, where an Israeli asset (maybe an Iranian working at the site who has been turned by the Israelis) uploads a program in person.
Israel needs the US. The US has several platforms that meet the range, payload and survivability requirements. For instance, take the B-2 bomber. The Spirit has the range (intercontinental with refueling), it has the payload (the upgraded MOAB type deep-penetrator), and it is survivable against most IADS (and definitely survivable against the Iranian IADS).
If the US does not assist Israel then Israel will have to opt for option number 1 (the suicide Sayaret excursion) or option number 3 (hoping that the Iranians are still susceptible to a Stuxnet type cyber attack), since option number 2 (a nuke strike) will simply not happen. Or they can opt for an air strike using a F-15/F-16 package similar to that used in Osirak. Due to the distances it would be a one-way mission as well, the Eagles/Vipers would have a horrific attrition rate even with jamming, and there is simply no (non-nuclear) bomb powerful enough that can be carried by an Eagle/Viper that can penetrate to the depth required to ascertain destruction of the under-ground facilities. The air strike doesn't meet the range requirement (unless they are very creative at aerial refueling, similar to how they fooled neighboring countries by speaking Arabic during the Osirak strike ....and even with all creativity in the world in regards to refueling it would only create an opportunity to reach the target but no fuel to make it back). The air strike can be survivable due to some good work done by the Israelis on using radars against themselves (not just jamming, but using the fact that a radar is basically a large radio transmitter), but the rate of attrition may be bad. The air strike most definitely fails the payload test, since there is no bomb the Israelis have that can penetrate deep enough, and considering the size of the deep penetrators used by the US there is no aircraft the Israelis have that can carry an equivalent weapon (they could jury rig a C-130, but it would not be survivable).
Cruise missiles launched from the Dolphin submarines have the range and are definitely survivable, but the cruise missiles do not have the payload. Again, if we are talking nukes its a different story, but using conventional explosives it is simply not sufficient. Even for blocking entrances and ventilation.
This is the reason why Israel is waiting. For the US.