If you feed them a proper diet, neither one has a strong smell.

The guinea poops less, because it is a smaller animal.

Guinea must be caged or in a ball, the rabbit can run free and will use a litter box.

If you do house train the rabbit and let it run around the house, be sure to “rabbit proof” your house – they like to nibble on cables and other things that could seriously hurt them.

Both animals require cleaning of their cages regularly. Failure to do so, as with other pets, will result in a stinky enclosure and stinky pet.

You should not be concerned about the amount an animal poops, as you would be cleaning their cages entirely every week or so, so the poop would not really last too long. I mean, you could fish the poops out of the cage to keep things smelling a bit nicer, but generally small pellet poop from these animals solidifies and loses its smell within a few hours.

I recommend that before you buy one of these animals, you do more research on both of them. Pet stores often have books regarding the animals they sell, and the people there will (generally) be knowledgeable (but never take what they say to be 100% truth, sometimes the people just make up stuff to sound like they know their things – I’ve been told outright wrong information about raising lizards which I then confronted the person about.)

Keep in mind that rabbits must re-ingest some number of their poop pellets, called cecotropes. Rabbits that are unable to practice cecotrophy will eventually suffer from malnutrition.

http://www.bio.miami.edu/hare/poop.html
http://www.threelittleladiesrabbitry.com/cecotropes.php