What is the best way to clean a throttle body on a 1996 Mustang GT 4.6L?

According to Ford, you're not supposed to clean the throttle body ever. The very best way is to remove the Throttle Body, use a spray cleaner made for Throttle Bodies, and use your finger and a rag or paper towel to wipe it clean. You'll probably have to reset the idle strategy when you're through.

What is the best throttle body cleaner to use ?

I don't know. You'll have to read some labels at the Parts store. The stuff I use at the shop is only commercially available. BG Throttle Body cleaner.

Agree with tracy. Just wanted to add using a tooth brush works really well to get what your finger cant.