Honestly? #2 wins hands down, IMHO. And let me tell you why.
I wouldn't even consider #3 to be an option because you would basically need to rebuild the vehicle from the ground-up to make it a front-engine, rear drive car in order to use the TH400 and BBC. By the time you do that, you won't have what I consider to be a "real" Fiero anymore. One of the things that makes the Fiero unique is the mid-engine, rear drive configuration.
#1 option is going to cost you quite a bit of coin just to get the engine in the car using a FWD-type transaxle (because of all the special adapters and custom pieces you will need). Then space is going to be at a premium in the already tight Fiero engine compartment. In addition, you won't have room to run the exhaust system the LS6 needs to breathe without cutting out the trunk. But I guess if you don't care about all of this, then this swap would be an option you could consider.
The L67 fits in the Fiero engine bay really well. It bolts right up to all of the popular FWD transaxles that can be used in the Fiero, and as you know the L67 can be built up to make an insane amount of power reliably.
I guess it all depends on what you want out of the car.