I think the reasons that alot of people think that Three Leaf Clover is better than all the heists in GTA V are that:
A. It's completely out of the blue, almost nothing in the game hints to you that you were gonna rob a bank.
B. It's the only heist in the game. After you've done it, There's nothing like it again in the game.
The reason that it came out of the blue was because Niko was basically just a gunman hired for a heist. He wasn't involved in the planning, he was just an extra hand, like all the crewmembers used in heists in V.
And people comparing 3 Leaf Clover to the heist missions in V is kind of ridiculous. As others have said there was nothing actually unique about it other than the bank job skin and the payout. The closest thing to 3 Leaf Clover in V is the Paleto Score and think about things it did different from other missions. Bomb squad suits, the minigun was introduced, it's the only mission where you use a bulldozer if I remember correctly.
And Universetwisters, you're blatantly wrong about the payout. The jewelry store heist alone gives Michael a million dollars if you play your cards right.