I would definitely avoid the tri-city area (Bay City/Midland/Saginaw). *Very* not crunchy except for some isolated communities--there's a crunchy Catholic community in Bay City, for example, but that doesn't sound like quite what you are looking for. For the most part this area is pretty heavily *******.
I agree that Traverse City is probably as crunchy as it will get up north, really from TC along the coast up to Boyne City/Petosky, but those are pricier. Benzie County is rural and *******, but immediately south of Grand Traverse County, much, much, much cheaper and a popular vacation spot as well. Pretty close to TC--like less than a 1/2 hour drive.
I'm not a fan of the Brighton area in general. Some Ann Arbor type folks, but mostly McMansion Hell. If you aren't into McMansions I would avoid Western Oakland County and much of Washtenaw County.
I agree that Ypsi is a good place place to look. Also as far Royal Satellites go, yeah, you'll not find anything inexpensive *in* Royal Oak, but look not only at Ferndale but also Pleasant Ridge, Madison Heights, Oak Park, Clawson, Berkley.
Ferndale is known for it's strong LGBT community and relatively inexpensive housing. It is adjacent to Detroit and gets a bit rough immediately adjacent to 8 Mile--lotta strip joints on 8 mile--but mostly it's cool. Pleasant Ridge is tiny bedroom community kinda between Royal Oak/Ferndale. Clawson is north of Royal Oak, a bit pricier but not as much as Royal Oak. Oak Park is the Orthodox Jewish corner of Metro Detroit--it can be a neat place and lots and lots of kids, but it's a fairly insular community too. Nice people though, and cheap. I grew up there, tucked into the corner of ten mile and greenfield. Oak Park as a whole is a *very* diverse city, and some great Arab groceries. Madison Heights is where my in-laws live. Very nice, family friendly. Very large Chaldean community in Madison Heights. Berkley is another bedroom community just west of Royal Oak. A bit pricier there I believe.
As far as schools go, the Oak Park schools are pretty bad, the Madison Heights ones are good, the Berkley ones are good, the Ferndale ones are mediocre, and the rest I don't really know about.
If you look at a map of the area it will look like I-696 runs right through most of these areas. Don't let that put you off too much. The freeway runs through a deep cement ditch with lots of bridges and parks built on top of it. Actually some very nice parks right on top of the freeway.
The Lansing area is mostly surprisingly cheap too, but I think you'll find that East Lansing is *so* overwhelmingly student oriented that it can get wearying. MSU is something of a party school to a degree--or at least it seems like it much of the time. Good school and all that, but huge and an enormous percentage of students there to party their way to a degree. Not nearly as college-towny is a positive, intellectual way as Ann Arbor/Ypsi.
The prettiest bit of the Lansing area and the crunchiest seeming (just things I've heard though, I've been there only a few times) is Haslett. Phenomenol schools though I've been told. Might be pricier. The suburbs south of Lansing are more rednecky, the ones East to North-East are crunchier.