How to Handle a Powergamer/Munchkin in Tabletop RPGs?

Tell your Referee to throw a bit more varied challenges at you. If every encounter happens at circumstances where you can just run up punch their face off, then it is a dull campaign, not a dull character. When you're facing a sniper 800 meters away with your head in the crosshairs, you will see that things will get a lot more interesting.

Tell your Referee to read the sidebars at pages 108 and 110 of the Cyberpunk 2020 rulebook. After a single session with those ideas, my players were much more careful with their new characters.

The Interlock system is deadly. It should be easy for your referee to make it just as deadly for you.

Whenever you are under fire, make a COOL+d10 roll against a target of 10(15 if you can't see/identify your attacker), modified by your stun/shock save. Failure means you can only run away or hide. Anything else is at a -5 penalty for the rest of your turn.

An alternative approach is, if you fail your COOL+d10 roll, you automatically repeat what you did in the previous round, regardless of if it is meaningful or not (e.g. you keep puling the trigger even if your gun is out of ammo)

Ok, first of all I'd like to say that making characters like this is one of the main reasons I role play, so I'll be trying to come at this from both sides where possible.

The first problem is the power divide.
The best way I've found of dealing with this is with making time the biggest problem.
Unless they have some way of manipulating time it is usually the most limited resource, as everything else can be gained given enough time.
If there is too much for him to handle then he will have to decide which things he wants to deal with personally and that will limit the occurrence of the problem situations of making combat encounters for everyone.

The next issue would be fame.
If he is so powerful then antagonists will start to hear about him and will start factoring him in when they plan.
You said he is taking advantage of an "Infection" in a way that it wasn't designed to be used.
A smart antagonist that knows a werewolf is coming to get him will hide during the full moon, or better yet, have wolfsbane.
Your antagonist can do interesting things like weakening, disabling, curing or more interestingly mutating your player.
This has the side benefit for a player that pays attention of showing that you are trying for them, catering to what they do so that they have a more interesting game.
The important thing is to not just surprise them with something permanently disabling as them they will just feel like they are being targeted.

If you must use rules then try to work out something works for both sides and is creative.
As you said, he's worked hard to get where he is, probably put a lot of time into a character that he really likes.
If you can, change the powerbase to something that works rather than just removing it from him. Also, do it with a story so that it doesn't break the immersion of your game.
For example have the players destroy an ancient artifact that was what was allowing all his powers to work together normally. As a side effect the powers, now in conflict within him, cause him to be luckier and so he gets a greater income or people become strangely attracted to him, causing him to have more helpers and influence in your area.

To directly answer the final question, either separate the objectives so that it is rare that he dominates and is ok when he does or create situations to bring him in line with others when it happens so that there is no divide.