The excessive elasticity in your muscles and joints during pregnancy due to the hormone relaxin is still present during breastfeeding. This hormone could possibly be responsible for your current knee pain. Also, if you're running your pre-pregnancy mileage with your now postpartum weight, your knees could be hurting because you're carrying the extra weight. Your body is still functioning as it does during pregnancy during postpartum, because of hormones still circulating in your system. Take your time and try walking with intervals of running first. Also, be sure to check with your doctor in case there is something else going on that you're not aware of.