If you can get a good engine builder to do it, definetly go with the rebuild. You know it's got all new consumables in it then (rings, bearings, oil pump etc). Just because the new engine has low miles doesn't mean it hasn't been thrashed it's whole short life, you may need to fix things soon down the track. If there are no good rebuilders in your part of the world go with the replacement, shoddy rebuild work is the worst. Another option may be an exchange engine, you give them your own engine and they give you a rebuilt one, makes it easy but costs a bit more.

Hope this helps.