Manitoba's got a relatively small land mass of traditional "prairie" farming relative to AB/SK, it's that rather than per area yields responsible for that stat - the area in SW Man. is comparable to perhaps the area south and east of Regina.   

The clay plain south of the Lakes (what's called the Red  River Valley, though it extends far from the Red) is considerably moister and with more reliable, hotter growing seasons, and supports cash crops more typical of eastern Canada than the prairies - the imaginary arid vs humid west vs east climate division that follows the Mississippi in the US, continues up into Canada roughly along the Pembina/Manitoba escarpment.   Lower wheat and canola yields because they're growing corn and soy instead.  Corn isn't insurable in most of Sask or AB and MB handily beats them in that category.