Well, this is one of those tough ones... what exactly do you define as a lake? What's a pond and what's a lake? Unfortunately, that comes into play a lot with this question...
Here's what I found:
According to the Wisconsin DNR, the state has 15,081 documented lakes and it has about 3,620 that are larger than 20 acres.
I'm finding a lot of sources saying that the total number of lakes in Minnesota is 14,927. The Minnesota DNR says that the state has 11,842 lakes that are larger than 10 acres.
If I could find a reliable source that told us how many lakes in Minnesota over 20 acres or how many lakes in Wisconsin over 10 acres, we would have good numbers to compare... but I think I'm going to stop here. :-)
My official answer is that both states have a WHOLE BUNCH OF LAKES.