Replying to professor who said that I can join his research group as a PhD student next year In search of a Ph.D. position, I emailed a professor and he replied me that I should recontact him next year as he does not have any available position right now. Also, he said that it will be too late for me as I will be wasting one year. Actually, deep inside, I do want to take a break of one year to spend some time with my family as I lived away from home for two years of my Master's study.

My question is, is it okay to tell professor that you want to take a long break before starting your Ph.D.? In other words, what is a proper reply to the professor who is saying that I should contact him next year?
He hasn't made any commitment to take you on next year. I would simply write to thank him for his consideration and say that you will re-apply if circumstances at the time permit. You don't need to say more now. 

Saying too much might be a mistake. But thanks should be expressed, certainly. Use the year to find another position or use it profitably otherwise. Reexamine your options if you are still available in the future.