I have white muddy water coming from my well, it is a drilled well about 250' deep, six years old and have never had this problem before. We have had a lot of rain over the last two weeks and might be the source but we have had a lot of rain before and not had this problem. Should I let the water run to try and flush it out or let it sit and settle?

I'd run it.

How long?

Kind of depends. If you have gotten a unusually large amount of rain the past couple of weeks, then it's possible the problem might persist for a while. As far as I know, the only solution is to keep running lots of water until it clears up. I don't mean 24/7 but three or four hours spread throughout the day.