[Radek]

It's underwater, on the bottom of the sea behind Anephas Shrine. If you have already found the way to the Pyramid then go to the beginning of the way, jump into the sea and swim east and little south. If you have just entered the area behind the Shrine then swim east and little south from the bay with the ship.
The Lost City is enough large so that it cannot be overlooked when you investigate the sea bottom.

Note: There are 2 entrances into the Lost City. One of them is near the 2 chests - this one is wrong (it's an exit in fact) and it does not allow you to enter the city. The right entrance is elsewhere.