You may have to test your well water to determine what is going on and what you need to do to be able to use it. Rainwater should be relatively clean unless you have some poor air quality.
Boiling no doubt will help kill of most pathogens, don't know how expensive it may get but cost will be a consideration with boiling.
A possible alternative or complementary approach is to expose the water to sunlight for for several hours then filter it. Sand and activated carbon which is often easily available. I know this is done for drinking water but I assume if it is good for drinking water, it could help with seed starting.