Use SPFServerManager.exe with the /recycle, sn:, and /all: arguments to recycle the application pools.
This example recycles only the server application pool for the site named SDx.
SPFServermanager.exe /recycle /sn:SDx
This example recycles all application pools for the site named SPF2016.
SPFServermanager.exe /recycle /sn:SDx /all:true