I live in Puyallup too. For natural food, I shop at Fred Meyer, Target, Tacoma Boys, Top Food and the Puyallup farmers market when its open. Occasionally, I'll make the trip up to Bellevue to go to Whole Foods and stock up. I've heard of Marlene's Market in Federal Way too but I haven't been there yet.
As far as midwives, I had Nancy Spencer in Bonney Lake as my midwife for my first pregnancy and she was wonderful. She has a lovely home with a birth center attached to it. http://www.lakesidebirthcenter.com/
http://www.naturalchoice.net/ is a great directory of natural options in the Puget Sound so that might broaden your ideas of what is available around here.
I don't think the areas you listed are very safe to live in unfortunately. There's drive by shootings and a high rate of crime. I wouldn't consider them family friendly at all.
I'd stick to communities like Puyallup, Bonney Lake, University Place, Brown's Point and the Proctor District in Tacoma, West Seattle, Bellevue, Mercer Island.