The Mad Mile ctOS center is on the end of the Navy Pier and is enclosed between two buildings with gates on each side.
While access to the area can be obtained through the lower level, the best entrance is through the scissor lift in the southwest side of the restricted area. From this entrance you can either snipe the enemies with a Spec-Ops weapon from a safe distance or get a good view of the area below before you make your way down the planters and sneak around the area to eliminate the enemies by hand.
Due to the closed in nature of this ctOS center, being caught will result in being surrounded and usually killed. It is best to be stealthy via a sniping spot or aggressive after finding a good cover position. If the guards begin to investigating the upper level where you are located you can always jump back into the scissor lift and use it as cover.