The "best" is combo the Xendrix/Herculean. Now best is since quotes because that isn't entirely true, but since I have access to the source code I've been sworn to a bit of secrecy.
Hopefully someone else will jump in and add the additional info.
The most damaging hand-to-hand weapon is indeed the Xendrix, although I'd argue the best is the Hydra-Jack because it doesn't need ammo.
The best long range weapon is the Trignet. Herculean is second best. Not only does the Trignet do the most damage, but if the shot is on target it disables the enemy for one attack, whether long range or hand-to-hand. This is pretty much the only way to fight guard clones and win. But that's another story...
The problem with the trignet is that only one monster carries it (Diabla, level 4) and only with one shot, so if she drops it you get a trignet with no ammo. The only way to use a trignet is to buy ammo for it in the afb research room at incredible cost: 95000 for 50 rounds. The trignet without ammo costs you 130000. I believe ammo and weapon prices in the research room are in the faq (which is in need of serious formatting help, btw).
Just to round out the combo, the best armor is Polycarbon. A few monsters have it, eg Orkaner in the AFB, or it can be bought in the same place as Trignet ammo.
If the Herculean really is the best long range weapon, wouldn't Overkill use it?