I've had both and love them! Guinea pigs are a lot more skittish and may go to the bathroom on you occasionally! They will bite if you accidently get your finger near their mouth. My hamster has never done either of these things. Guinea pigs smell worse in my opinion but i love both! If you get a hamster I reccomend a long haired male teddy bear hamster. Good luck!

Guinea Pigs, in my experience, are noisy, run, don't climb, are pack animals, a little bit messy, very docile and cuddly when trained right and fairly large as far as rodents go. They are native to the Ades if memory serves. A guinea pig is a lot larger than a hamster. Hamsters, also in my experience, are small, often nippy, tiny, clean, fairly quiet, skittish and hyper active. Similar personality wise to a mouse, but a very different look.

 Hamsters run on a wheel in their cage. Guinea Pigs do not. Hamsters DO NOT eat citrus fruit (lemons, limes, or any other citric melon) this is harmful to Hamsters. On the other hand, Guinea Pigs need Vitamin C. That's why you put two drops of Vitamin Drops (found in most pet stores) Guinea Pig's water. You put two drops PER OUNCE of water. Hamsters crawl in tubes, run on wheels, and are active in their cage, but not usually easy to cuddle. Guinea Pigs don't do much in their cage, but they get attached to their personal owner and recognize them and they cuddle!!! Hamsters tend to be faster. Guinea Pigs tend to be slower. HAMSTERS SLEEP IN DAY! (alot of people forget that) and Guinea Pigs sleep at night. 
The list goes on and on. I've done alot of research on both. They have some great care books on both of the Species at petsmart