Ideally in the middle of your rotations. Beginning of 3rd year you are in unfamilar territory, trying to learn how to do H&P, SOAP notes, present patients, follow-up. If you do medicine or peds, you will be spending some of your energy trying to learn basic skills.
Middle of MS3 - you still have energy and you've handled the basics.
End of MS3 - not a major issue if you do peds or medicine towards the end. However, if you discover that you hate medicine or peds, end of MS3 is hectic in trying to schedule electives in fields that you may be interested in but have not experienced as a 3rd year (anesthesiology, ortho, ENT, optho, rads, etc)
One thing to keep in mind is that Pediatrics is seasonal - you will see more of one disease during one part of the year, and another disease during another part of the year.