I use this thermometer:
http://www.thermoworks.com/products/handheld/mtc.htmlwith the Thermoworks Miniature Needle Probe Model 113-181.
The probe is fine enough to allow it to pierce the bag and measure the temperature at the centre of the food.
The way this is achieved is to stick a small piece of high density foam tape to the pack and to pierce the bag through the foam tape into the food
The probe also uses a standard "K" type plug so I can use it to attach to my data logger as well.
Hope this is useful,
Peter.