You may be asking for too much.
Since a steam system is open to the atmosphere and constantly rusting and corroding, it's very difficult to keep the water pure. You should always expect some discoloration of the water. The problems begin when the water gets dirty enough to cause priming and foaming. That's when you should follow the boiler manufacturer's cleaning instructions.
Another consideration is that the Old-Timers used to drain their boilers during the summer because the water left in the boiler would evaporate up into the pipes and cause rust. This rust washes down into the boiler at the start of the following heating season. If you're using the boiler during the summer to make domestic hot water, you won't be able to drain it, of course, so you'll have to deal with the dirty water.
The installer didn't clean the boiler.
Boiler manufacturers use a lot of oil when they drill and tap the boiler. The installer also uses oil when he threads his pipes. If you don't get rid of that oil, the boiler water might not only appear dirty, it will also prime and foam.
Here's another thing to consider. New boilers act like scouring pads on old steam systems. The dry steam will reach out into the system further and faster, and dislodge years of dirt and corrosion. When that grime washes back to the boiler, the water will appear very dirty. You may have to clean a replacement steam boiler more than once. Follow the manufacturer's directions.
The buried returns are leaking.
The condensate flowing out of a leaking buried return will create mud. The flow of condensate can carry some of that mud back to the boiler where it shows up as filthy water in the gauge glass. If you've cleaned the system repeatedly and still wind up with dirty water, suspect those buried wet returns.
And even if the water isn't dirty, suspect them anyway. Buried wet returns are always worthy of suspicion.
The system is taking on too much feed water.
Fresh water contains lots of oxygen, and oxygen causes corrosion, which shows up as rusty water. Feed water also contains minerals that will settle out when you heat the water. Those minerals (mostly calcium and magnesium) form a rock-hard scale that can quickly clog your return lines. That forces water up into the returns where it meets steam and creates water hammer. The water hammer can dislodge even more corrosion, which eventually washes down to the boiler and discolors the water. When these things begin to happen, dirty water is usually the least of your problems. Find the source of the excess feed water and get rid of it.
Want more troubleshooting tips? Check out A Pocketful of Steam Problems (With Solutions!).