I'm looking to get a directory of Dairy Farms in Wisconsin and Minnesota and the approx. size of each farm in heads terms? Any idea where can I get this info?
The Census of Agriculture, National Agricultural Statistics Service (NASS), and the ERS (Economic Research Service) branches of the USDA have most of the data you are looking for. However, I'm not sure if you can get down to the farm/number of heads level, although you should be able to get pretty close.
You can get a good feel for this here:
Ag Census Web Maps lets you mash them all up and get a better view (in my opinion). Here's a screenshot of Average Number of Cattle and Calves per 100 Acres of All Land in Farms: 2012
Lastly, try states agricultural services website; Wisconsin's has a directory