Make sure it's installed in the correct location. The folder structure should look like this:
{sketchbook folder}
|_tools
|_ESP8266FS
|_tool
|_esp8266fs.jar
You can find the location of your sketchbook folder in the Arduino IDE at File > Preferences > Sketchbook location.
I just installed the latest version of ESP8266FS (0.4.0) and it shows up as Tools > ESP8266 Sketch Data Upload in Arduino IDE 1.8.9.