Omega comes after the Cerberus Coup, as I said before, Shepard is very angry and takes the opportunity to kick some Cerberus butt in retaliation over the attack and out of rage at Thane's death. The way I envision it, after coming back to the Normandy but before going off with Aria's fleet, there should've been some sort of conversation with Garrus or Liara or Joker about it being too dangerous to go off on this one. Especially alone, reminding Shepard that his last major solo mission ended in the destruction of a mass relay and him being up on charges for it.
Leviathan usually starts right after returning from Omega at the citadel, do the beginning and then return to it on the way back from Rannoch. I typically will try to squeeze in the ardat-yakshi monasary in there somewhere before the mining colony so banshees have been revealed.
Citadel I do at the end. It makes the most sense to do it after Horizon to me. You're prepping for the final battle, the ship needs an overhaul before you go. The endings are crap, I'm sorry to be blunt, but they are. So the party is after the Earth mission and the starbrat lied, EDI is not dead, the citadel was repaired, Thanks to the Geth, they didn't die either. After the party, Shepard is thinking about the challenges ahead of rebuilding the galaxy, will the alliances hold? What threats do they face given the heavy losses in the war? Will his crew have to go their separate ways?