One of the best mustang engines ever made was the 429 cobra jet, kind of rare but alot cheaper than trying to adapt a newer style engine in to a old beast. just about any older carbed engine will work fine.
If you mean which stock Mustangs are the fastest, then it's definitely going to be the 2010 Mustang. They add power ever generation. I would go with a current Mustang, 08-09, GT or GT500 engine. They are the most reliable engines more the Mustang and have the most power.
the 427 they put in the 70 boss is the best stock motor but if you can find the old not new 429 itercepter that is the most awsome thing in the world when you turn that thing over you will turn the heads of anyone in hearing range