If you want it to move stuff around, the 8ft bed is always going to be better. It's a trade-off though, because you're going to give up something to get that bed, whether it be cab space (if you want the truck not to be so long, you'll need to shrink the second row), gas mileage (bigger is worse), or the ability to park in normal sized spaces and garages (if you keep the full size cab AND the long bed, the vehicle overall is VERY large).
As long as you want the bed more than you want the other stuff, then go for it!
And frankly, even if you go for the 8 ft bed + extended cab, you'll still probably end up shorter and with better mileage than the box truck!
If you're going to be moving just one or two machines at a time, then a 6 foot bed might be OK for you - you can stand them up and strap them down (if two machines), or you can just lay it on it's back (for a single machine).
Have you considered keeping the box truck for moving stuff and getting a smaller car for day-to-day? I don't know your normal operations, so that might not make sense for you, but it's something to consider.
You could even consider a small truck and a flat-bed trailer. That lets you move a few smaller items, gets you good fuel economy, and lets you tie on a bit more space when you need it. Just make sure the vehicle can handle towing a good side load and you're golden. You can even just rent the trailer from u-haul as needed - it's a little more planning, but it saves you having to maintain the thing.