There are a total of 5 workbench tools
Tool #1
Location: Bill's Town
The first set of Tools can be found in the Graveyard segment of Bill's Town. At the very beginning of the segment, you'll find yourself in the basement of Bill's church safehouse. Opposite the workbench Bill creates the Nail Bomb on, you'll find the Tools in a corner.
Tool #2
Location: Pittsburgh
The second set of Tools can be found in the Alone and Forsaken segment of Pittsburgh. After the ambush at the very beginning of the chapter, you'll head into a garage littered with corpses. Near the shutter door, you'll find the Tools.
Tool #3
Location: The Suburbs
The third set of tools can be found in the Sewers segment of The Suburbs. After Joel helps Ellie, Sam and Henry cross the sewers' sunken room, you'll enter a long tunnel leading to a set of double doors. Midway down this tunnel is an open doorway on the left. Inside the room behind the door are the Level 3 Tools.
Tool #4
Location: The University
The fourth set of tools can be found in the Science Building segment of The University. When you first arrive in The Science Building, head to the end of the second-floor corridor. The final door on your right will be a Shiv Door. Inside, you'll find Level 4 Tools.
Tool #5
Location: Highway Exit
Found in the Highway Exit segment of the Bus Depot chapter. After petting the giraffe, descend the stairs and reach the area with the medical tents. In the central tent, you'll find the Level 5 Tools. If you've got all the tools available then the For Emergencies Only trophy will unlock.
Source:
https://www.ign.com/wikis/the-last-of-us-part-1/ToolsIf you'd like to follow a video guide, check out PowerPyx on YouTube: