Traveller Hotel is like the cheapest in the downtown core.
It's on Riverside just east of Ouellette so you are in the heart of everything. I bet it fills up quick though so you may want to make a reservation before hand.
Travelodge Hotel Windsor Downtown
Phone: (519)258-7774
33 Riverside Drive East, Windsor, ON N9A 2S4
MAP to Hotel BTW: i'm from windsor so I can get you more info if needs be...