Now that I am on a computer and not on my phone I will type a bit of a better reply...
IMO, rock the NV3500! Like Vinnie said, the newest transmissions are miles ahead of the older versions. They don't fall out of gear, have much better designed internals and are considerably stronger.
I had a 96 pickup with an NV3500 in it that I did have suffer a failure. It started grinding really badly in 2nd gear and made an awful whining noise. When I pulled it out and took it in as a core for a new transmission the shop told me that the reason why it failed is that it had been filled up with 80w90 gear oil instead of the 5w30 syncromesh fluid it is supposed to run. Sure, it was behind a 4.3L V6 but I beat the crap out of that transmission and never hurt it.
My next experience was putting one into an old K10 I had on 35" boggers with 2.73 gears and a naturally aspirated 6.2L diesel. That truck couldn't maintain speed in 5th gear even at it's top speed of 58mph. The engine just didn't have the power to overcome the crappy gearing. I beat the ever living crap out of that truck offroad and never hurt the transmission at all. I later swapped the NV4500 I had in my old K25 with the same 35" boggers, 4.56 gears and a turbocharged, souped up 6.2L diesel with the NV3500 from my K10 because I hated the gear spacing in the 4500. Again, I flogged that truck which had much more input torque than the transmission is rated for and never hurt it.
Then I swapped that entire drivetrain over into a K5 with 37" boggers and again flogged it without ever hurting it.
I sold the K5 with that drivetrain in it and he drove it on the highway something stupid like 10hrs home and it was the rear driveshaft that failed. Not the transmission.
I have a good understanding that the earliest Getrag HM290s and the earliest NV3500s did have issues that gave them a bad name, but the 96-98 and especially the 99-07 NV3500s are a totally different animal. They'll hold up to some abuse before they fail. Yes, you can definitely break one if you try but if you have any sense in how you drive it then it'll last.
The ZF6 is definitely a decent option if you are considering a high power engine or plan on shock loading the drivetrain regularly. Even they suffer from a weak input shaft and occasionally their housings will explode under shock loading. They have a great gear spacing like the NV3500 and shift very nicely. They have a granny low like the NV4500s in the 5. something range and a decent OD gear of .73ish. They will swap into place of an NV4500 being the same overall length from bellhousing to tailshaft. They use the same clutch and input shaft as the NV4500. The top side of the transmission is roughly the same height as the older transmissions but it is quite a bit deeper. The NV4500 has the tail shaft adapter on it with the 5th gear inside which is where the ZF6 fits the 6th gear hense the same overall lengths.
The biggest issue with the 29 spline output shaft. You need to swap the input shaft on an NP241 from a NP261 to make it fit. The part that makes that tough is that somewhere in there the planetary gears were changed and I am not 100% sure that the newer input shaft will fit into the old pass side drop 241 cases.
All in all, I'd go NV3500 first. If you break it, then you already have everything in place to simply swap the ZF6 in and convert a transfer case (or install an aftermarket piece)