Hi Gogden,
I have you tried hooking up the thermocouples differentially? This might eliminate the problem. Also, if you could give me some more information about the noise it might help me troubleshoot the problem better. Sometimes theres some noise due to lower quality power connectors on some laptops. This is typically associated with a 60Hz noise. Most of this is seen through a small audio hum when trying to amplify audio coming from laptops but it might be affecting the grounding of your USB DAQ card. You might try one of these audio hum eliminators around which may solve the problem. If you search google for "audio hum eliminator", you will find a variety of products for it. In conclusion, I would first recommend trying differentially and if that doesn't fix the problem you might look into the ground loop eliminator products out there.
Regards,
Paul Cason