Do i stop running until my baker's cyst is gone, or can i start running now that it's down to ping pong ball size?

Depends: A baker's cyst is an extension of your knee joint. The fluid from your knee becomes trapped within the cyst behind your knee whenever the knee is irritated. It is a reflection of damage within the knee. If your knee consistently swelling with running, then the cyst will increase in size. It takes time for this to resolve. If you are tired of this, consider getting it checked by an orthopedist.

Depends: I suggest that you use your pain and symptoms as a guide. If the cyst is decreasing in size and your symptoms (eg pain) have resolved, then it is time to slowly get back to your normal activities, including running. Start slowly and add volume and intensity as long as the cyst and pain do not return.

Go running: Half the time the a baker's cyst is associated with a torn meniscus (cartilage) in the knee that will need attention, but the other half of the time it just happens. Frequently the cyst will enlarge in size when active and decrease in size when sedentary, but if it doesn't bother you, go running. Sometimes they will rupture by themselves - painful but safe and problem solved.