I believe there are quite a few members here with a bigger dog and a Yorkie. I only have my Yoda, but have you tried getting down and playing with both of them at the same time? Maybe the Yorkie is a bit scared and not quite sure what to think of the 'big' puppy. Maybe take them on walks at the same time? Or just try to get them used to each other. Will they play fetch together if you throw something and have both retrieve it? I'd say it just takes time and the more interaction they have, the better off they will be, but for the first few interactions, be there with them to make sure nothing bad happens.
