Big block with manual transmission recommendations

I would try to expand your year range one year to 2001. Then you can get a Chevy with the awesome 8.1L and a 6 speed or the excellent Allison auto. I've owned 3 Chevy's with Allisons: '01, '05, '07. They have all been flawless and these are work trucks that haul and tow hard.
The 8.1L is certainly my choice for a big block. The one in my '01 dually is quiet, smooth, reliable, and powerful.
With a 2001 2500HD or 3500 truck you will also get other upgrades of frame, brakes, etc. that will help in towing.