ID Card 46: It's on a desk in the pump control room, where you cut the water flow for the Let the Waters Flow quest. During your first visit to the Sewers.
ID Card 47: After getting the ID Card 48 keep advancing until you reach a big room with 2 doors on the left side. The Id Card is in the first one, on the workbench.
ID Card 48: In your first visit to the Sewers, follow the path to the Town Hall until you find a room with 2 cell-like short tunnels on the left side. The ID Card is in the first one, on an open grey suitcase.