If you really like the Duncan 59 there should be no replacement for it, because you won't find anything like it. In the quest for tone, you should be more concerned about how you can get the money to buy a Duncan 59 rather than a replacement.
There is no DiMarzio direct replacement. If you want to try a sweet
neck pickup, I suggest the PAF Pro or the
Air Norton. Air Norton (modified)/D Sonic is what Pettrucci uses.
It'd also help if you could tell us what kind of tone you're looking for, body and neck/fingerboard woods, etc.