You can definitely see the Maid of the Mist boats from the observation tower.

Yes, and it’s a great view. From the Skylon Tower or the Niagara Falls observation deck, the boats are below you, heading toward the base of the falls. The angle is roughly 30 to 40 degrees downward from eye level — think looking down at a sidewalk from a 10th floor window.

You won’t see them straight down (that’s the edge of the falls), but off to the side, circling near the base. Best spot is the north-facing side of the tower. Bring binoculars if you want to see the ponchos clearly.