Aha! That's the deal.
Okay...Nivius' tomb is located right behind the Ratkeeper in the lower level of the crypt. You can't get to him from the Ratkeeper side though...you have to swim through from the Asylum down through the tunnel and emerge in what is called the "Tomb of Heros".
To open his tomb, swim down the water channel on the northern side of Rethpian's (the ratkeeper's) room, and look for a small key at the bottom near the grate. Pick up the key and swim back. Now go to the west door; that's the Tomb of Nivius. Open the lock with the key, go in, hear Nivius' speech, and agree to take the Oath of the Mavin. The Signet will appear just to the left of his corpse after you take the Oath.
-Sazerac