I have said similar things in the past in regards to new born's especially, such as, "She looks like you when she gets cross," sometimes they have looked more like one parent whilst relaxed, but when pulling a grumpy face or crying have looked more like the other, but I have never intended my comments to cause offence, and usually chuckle when I have said it. Admittedly the parents I have made these comments to have usually been family members and know me very well as I am a bit of a joker anyway.
I think I would ignore it for now, she may not have intended for the comment to sound so harsh, plus you will be more emotional for several months after giving birth. If she persists in making tactless or cruel comments be straightforward and upfront with her and tell her you find the way she speaks to you offensive or upsetting and just keep your distance without removing your baby or her son from her life, let your son make any decisions on how he deals with his mother, but tell him how you feel. Try not to do any of this whilst angry or upset as that could be seen as you overreacting. I hope you manage to find a solution to what could be a very unpleasant situation. 