A tower, of course, is any tall, high structure (in comparison to its width and length) on any building. I am not certain if you are looking for a particular word or just looking for a synonym, but several other structures fitting that general term could be considered small towers.
The most likely, and probably most often-used, synonym for "small tower" is turret: "a small tower or tower-shaped projection on a building." In castles or other medieval or Gothic structures, turrets are the highest, smallest towers on the structure.
A spire or steeple is a kind of small tower perched on top of a building, such as a church; and a watchtower is a small observation tower used to, of course, watch for things such as fire, inclement weather, or an approaching enemy.