We have used
http://www.jandmgolfcarts.com/engines.htm , they specialize in golf cart engines. There are others out there if you look. Sometimes a good local machine shop will do well, but they may want you to track down the parts, which could possibly save you some money in the long run. I did a quick glance through this site's sponsors and didn't see any rebuilders specifically mentioned, but I could have missed something. I'm sure someone will let us know if I did.