best program without a doubt would be Worldcraft 3.x as it was developed specifically for Half-Life ... but personally I'd use Qoole instead, its far better and easier.
Don't make a world within something like Max unless you know what your doing because its FAR too easi to develop a world with leaks ... Half-Life doesn't like rendering them and your system will die when your crosshair is over themm people who understand the engine know full well why
For Quake3 on the other hand Gmax is outstanding for developing levels for it, GTKRadient has alot of good addons which will also extend the usefulness of Radient however does take ALOT of getting used to
Gmax is more for the idiots of world creation, but the fact you have modelling tools also at your disposal helps greatly.
Anata aru kowagaru no watashi!