The CT3 is needing new rear brake shoes. Could someone please point me to a few decent options. I couldn't find much in my searching. Thanks!

Search your model on CMSNL or Partzilla and they will show you the current Yamaha part number.

Take a little care removing and disposing of the old ones, as they might contain asbestos.  

Thanks for suggesting this. I tried to search by part number and not much came up. A pair of SOK brand shoes on ebay is all I could find. I wasn't sure if the CT3 shoes were compatible with other models, this would help open up search options. 

Original part numbers have been superseded (changed) many times over, and the two sites that I suggested should have the current numbers. Your local bike shop, if you use one, should be able to order them from Yamaha, or their regional wholesaler. If not, buy online at ebay etc.