I started getting them at the Cantina by Mexico, that became too crowded and besides it is now closed for renovation. I next started getting them from the cart near World of Disney. I didn't notice a difference. I even got some at MK and again I didn't notice much difference. The key issue is the freshness, they tend to harden if they sit too long.
I think at the Cantina by Mexico they are a little fresher than other places. IMHO, WDW Churros aren't great. They taste like they've been sitting around for a while.