Is well water a homogeneous mixture?

Yes, well water is a homogenous mixture, or solution. Tap water is also a solution. Only distilled water is pure water.

Generally, yes: the water would be essentially the same no matter how you drew it.

One exception might be if the well was abandoned: over time, particles and minerals that would normally be suspended (floating) in the fluid would have a chance to precipitate out and settle to the bottom of the well. If that happened, the mixture would have become heterogeneous instead.