Where is the fake sword?
The last we see of it, it's still in Bellatrix's vault (emphasis mine):
Harry shone his lit want around the vault: its beam fell upon glittering jewels, he saw the fake sword of Godric Gryffindor lying on a high shelf amongst a jumble of chains.
Deathly Hallows Chapter 26: "Gringotts"
It is possible (even likely) that the sword was removed from the vault by the subsequent avalanche of fake treasure (emphasis mine):
The tiny golden cup, skewered by the handle on the sword's blade was flung into the air. The goblin astride him, Harry dived and caught it, and although he could feel it scalding his flesh he did not relinquish it, even while countless Hufflepuff cups burst from his fist, raining down upon him as the entrance of the vault opened up again and he found himself sliding uncontrollably on an expanding avalanche of fiery gold and silver that bore him, Ron, Hermione into the outer chamber.
Deathly Hallows Chapter 26: "Gringotts"
However, presumably the goblins have means of getting everything back where it belonged; their security system wouldn't be very effective if they couldn't clean up after it, after all.
The fake sword never appears after this
Where is the real sword?
This is unclear. The last we see of it, Griphook is carrying into the middle of a crowd of angry goblins:
Hardly aware of the pain from the burns covering his body, and still borne along the swell of replicating treasure, Harry shoved the cup into his pocket and reached up to retrieve the sword, but Griphook was gone. Sliding from Harry's shoulders the moment he could, he had sprinted for cover amongst the surrounding goblins, brandishing the sword and crying, "Thieves! Thieves! Help! Thieves!" He vanished into the midst of the advancing crowd, all of whom were holding daggers and who accepted him without question.
Deathly Hallows Chapter 26: "Gringotts"
We don't see it again until Neville pulls it out of the Sorting Hat:
In one swift, fluid motion, Neville broke free of the Body-Bind Curse upon him; the flaming [Sorting] hat fell off him and he drew from its depths something silver, with a glittering, rubied handle - The slash of the silver blade could not be heard over the roar of the oncoming crowd or the sounds of the clashing giants or of the stampeding centaurs, and yet, it seemed to draw every eye. With a single stroke Neville sliced off the great snake's head, which spun high into the air, gleaming in the light flooding from the entrance hall, and Voldemort's mouth was open in a scream of fury that nobody could hear, and the snake's body thudded to the ground at his feet.
Deathly Hallows Chapter 36: "The Flaw in the Plan"
In absence of other information, we have to assume that the goblins were keeping it somewhere secure. In any case, there are no longer two swords of Gryffindor floating around, which leads me to the next question:
Is Snape in danger of being discovered?
Probably not. As far as Bellatrix knows, the sword that was in Harry's possession was the fake:
"How did you get into my vault?" they heard Bellatrix scream. "Did that dirty little goblin in the cellar help you?"
"We only met him tonight!" Hermione sobbed. "We've never been inside your vault.... It isn't the real sword! It's a copy, just a copy!"
"A copy?" screeched Bellatrix. "Oh, a likely story!"
"But we can find out easily!" came Lucius's voice. "Draco, fetch the goblin, he can tell us whether the sword is real or not!"
Harry dashed across the cellar to where Griphook was huddled on the floor.
"Griphook," he whispered into the goblin's pointed ear, "you must tell them that sword's a fake, they mustn't know it's the real one, Griphook, please -"
[...]
"Well?" Bellatrix said to Griphook. "Is it the true sword?"
Harry waited, holding his breath, fighting against the prickling of his scar.
"No," said Griphook. "It is a fake."
"Are you sure?" panted Bellatrix. "Quite sure?"
"Yes," said the goblin.
Relief broke across her face, all tension drained from it.
Deathly Hallows Chapter 23: "Malfoy Manor"
It probably should have seemed suspicious that, despite claiming it to be a fake, Griphook continues to hang onto it for dear life; then again the Death Eaters aren't exactly known for paying attention to the "lesser" races.
Bellatrix presumably believes the real sword is still in her vault, so Snape's cover is secure.
However, even if it came to light that the sword in Bellatrix's fault was a fake, that wouldn't necessarily blow Snape's cover. It's revealed near the end of Deathly Hallows that Dumbledore had hidden the real sword inside his office, while leaving a fake on display (which is where the fake originates from, remember):
[Snape] approached the portrait of Dumbledore and pulled at its side. It swung forward, revealing a hidden cavity behind it from which he took the sword of Gryffindor.
Deathly Hallows Chapter 33: "The Prince's Tale"
If the fake was discovered, Snape could have easily absolved himself of suspicion by telling the truth: Dumbledore planted a fake sword, and everybody (including him1) was taken in by it.
1 I never said he had to tell the whole truth...
