Something tells me Tommy's pent up rage and talent for surviving the odds would win him the battle, he was ambushed by eleven men and killed them all, he's not stupid either so it'd be tricky for Niko to get the better of him unless he takes advantage of Tommy's anger issues and uses it to lead him into a trap, even then Tommy would probably come out still breathing. It's not like Niko would go down easily either though, he can be pretty rage fuelled, he'd have his marksmanship training from the military, but then it might come to nothing considering Tommy has the more accurate rifle: the M4.
If Vercetti could land a hit on Niko with the Python, he'd be done, but Niko could spam the hell out of his Glock and overwhelm Tommy with his additional bullets, he only needs to hit Tommy once in a vital area to kill him.
With melee weapons, the machete has a longer reach but Niko would probably have some experience with a combat knife so he could get in a fatal stab if he was quick enough. You have to remember how vicious Tommy is though, he'd be swinging it like a butcher and he never backs down so I think he'd be a pretty tough melee opponent to beat.
With heavy weapons Nike might have an advantage, all he'd have to do is get the drop on Tommy or his gang, and he could blow them away with one blast. However if Vercetti opens fire with the M60 before Niko gets a chance to aim though it could pretty much wipe him and his allies out if they didn't have enough cover.
All in all though, I think Tommy would win, he's the Harwood butcher, Niko may be a war veteran with good understanding of weapons and tactics but Tommy is no stranger to weapons either, and his psychotic rage combined with automatic and more accurate weapons such as the M4 would probably mean that he would come out on top. I think Niko and his allies would take down most of Vercetti's henchmen though before Tommy wipes them out though.