Well if you want to get down to stats, there are many more situations when the winning run is on first, second or at the plate than on 3rd base. Also, the only time a pitcher might possibly want to face Ortiz with the winning run on third would be with 2 outs. With no out or one out, the pitcher would fear Ortiz, because he is more likely to drive the ball far enough to get the runner in.
So let's recap. All pitchers would fear Ortiz more than Jeter if the winning run was on any base with less than 2 out; all pitchers would fear facing Ortiz more than Jeter with the winning run on first, second or at the plate with 2 out; and not all pitchers would fear Ortiz more than Jeter if the winning run was on third and 2 outs. In conclusion, Ortiz is more feared than Jeter in clutch situations.