IMVHO - I say 1 or 2 also.
A crate engine will have a warranty (unless it excludes the LS9) from GM and you know everything is about as good as it's going to get from the factory. It's precision built and hand assembled. They check it before it goes out the door so it's not likely you'd have a problem down the road. However, I remember reading that engine is at it's limit, at least per the engineers. I don't know if that means durability, emissions, or fuel efficiency (or a combination for that matter) but it's got a lot of good stuff in there.
Rebuilding the LS3 I think is a good alternative too. It's mostly the same block as the LS9, minus the oil squirters and bigger head bolt holes. The heads on the LS9 (and LSA - I think) are different as they are rotocast and heat treated to a different specification (I suspect) to minimize distortion under boost. You could just throw a Lunati reciprocating kit in there and be good.
But if you go to that extent, why not consider an LSX block, either GMPP heads or some aftermarket heads, and go with a forged set-up? You have room to grow with that block, and you won't have distortion issues as one would with the aluminum LS-engines, but it'll probably extend your budget more.
I think that that LS3 will live with some moderate boost though without much trouble for a long time. If you're just going to be playing around and not beating it up on the track then I think this would be a great way to go.
Since it looks like a Z06 was your original plan, I think you can easily spend the money in the difference between the cars and build an even better Camaro. With as much support there is from GMPP and the aftermarket you're going to be covered however you want to build it. Please do me a favor though - keep us posted on what you eventually plan and how things come out
