Even the small one will be big for a 3-pounder, but she may grow into it. There is a puppy version that is blue/white. You can put something in the small end of the cone to plug the hole -- a liver treat or a piece of apple. Then you can fill it with whatever you like. The squishier and smellier, the better.
The only problem we have is that if Milo gets a treat that he is REALLY excited about, he waits until I am home before he eats it. So, I do a lot of Kong stuffing to try and help him occupy him when I'm gone that goes sort of, well, by the wayside. He waits til I am home unless I give lower-priority treats.