Try not to worry too much. I have had two healthy babies (5 years and 11 months old) while having lyme. I have had lyme since 1998. I wasn't able to be treated while pregnant because I was extremely sick with hyperemesis so I couldn't eat or keep anything down. I know lyme can be passed to the baby, but from all I was told both by my lyme specialist as well as two high risk ob's, the risk was small. Of course I am grateful that my daughter's are both healthy. The hardest part is dealing with a chronic illness while trying to take care of a new baby (no sleep, etc...). But try not to stress too much either. Work on finding a lyme literate dr that can work with your ob. You can have the baby tested at birth to ease your mind too.
You will be ok. The good news is that I felt great after giving birth with both my daughter's for about 6 months. The lyme symptoms came back, but they tend to disappear during pregnancy and for me, the months following. I am also still nursing. I plan to stop at 1 year if my daughter will cooperate with that decision. lol.
I wish you all the best. If you have any questions feel free to ask.