Unfortunately, there's not enough research into these infections being passed in utero or through breastfeeding. I was one of the lucky ones, in that I was pregnant and breastfed 2 kids before finding out what was wrong and getting my diagnosis (my kids were actually adults by this time) and after a few early childhood issues, they have been healthy and fine (although I still watch their health very closely!!).
There's no way to know what the chances are, we just feel like most any chance is too high to be passing something as horrid as these infections on to our kids!
This is one site that has a lot of really good information on kids with Lyme, particularly helpful for trying to determine if a young child (like yours) has these infections:
/sites.google.com/site/drjoneskids/home And, we do have a handful of mothers with sick kids on here that can also be a huge help to you! I'm sure they will be along soon to help give you some more ideas and help.