Difference is slight.
Thanking a person is in words expressed form of showing appreciation to that person:
Friend helps you at work. You tell them: "Thank you for helping me."
Appreciation is more than just expressing thanking. It is when you feel respect to person due his actions that effect you directly or indirectly:
Friend helps you at work. You appreciate it.
Friend helps you at work. You show appreciation with gift.
Friend works with you. She has a lot of work. You ask her to help you. She accepts. You tell her: "I really appreciate that". After work is done you may tell her: "Thank you for your help"
I hope that explains.