They are same, both mean "an hour", no different. But 小时 are more formally. You should use it in an official situation. 钟头 will be improper in those case. e.g. 经过一个钟头四十分钟的激战,客队获得了胜利。 That's definitely awkward. 经过一小时四十分钟的激战,客队获得了胜利。 This would be better.
On the other hand, 钟头 are more orally, and should been used with measure word (classifier) "个". e.g. 你多久能做完这三张试卷. 两个钟头.
If you are not so confidence with them, always use 小时. It's the best choice in most of the situation. But it will make your tone more official, like a lawyer.