As one of our resident Bostonians, here we go:
Granite Links is a fun time, a pretty course, but not much to write home about architecturally. It plays on top of part landfill, and part filled-in quarries, but the few remaining pits don't really come into play. Also, the $95 price tag is tough to swallow for such a course.
Pinehills is also nice, I like the Nicklaus slightly more than the Jones, but it's cartball, up and down the glacially-formed sand ridges in the areas. Also $90.
Redtail is fantastic, I have to get back there. It's a bit out of the way, in Devens off Rte. 2, but it's cheaper and much better than the previous two.
Wachusett is awesome as well, a Ross course that feels like the Boston private Ross courses. It's in West Boylston, out near Worcester, probably 45 mins-hour west of the city.
Waverly is fun, part of Silva's early Raynor-influenced design. You will come away shaking your head at a couple of the holes, but even the strange ones are fun.
Cyprian Keyes is ok, although many holes are claustrophobic, and some of the elevation changes do not fit the design.
Stow Acres isn't a bad layout, but it's 60's architecture where the trees need to be pruned back a bit.
I thought Shaker Hills was a nice course, fair, like what Cyprian Keyes could have been with better use of the rocky hillsides.
My ranking of those mentioned:
Redtail
Wachusett
Waverly Oaks
Pinehills (Nicklaus over Jones for me)
Shaker Hills
Granite Links
Stow Acres (North)
Cyprian Keyes
Other courses worth a look:
Franklin Park: Yes, a muni, but a Ross-redesigned one at that with lots of history and a nice new clubhouse. Bobby Jones practiced here in the field adjacent to the 12th hole while at Harvard Law. A bunch of fun holes in conditions that are not exactly sparkling, its worth it just due to the fact that it lay fallow for close to two decades before it's revival by the locals in the 80s. This course is also close to the city (about 5 miles), and it is worth noting that its in an area where bicycle cops patrol the course parking lot. If you can look past all of this, its a fun experience.
Atlantic: Another good course in Plymouth that is cheaper than Waverly and Pinehills with pretty much the same land and style.
Blackstone National: A bit further from Boston, the course is South of Worcester, and reminds one of the Plymouth courses with combined open and treed holes.
Also, as a quick note, this is aeration season in Mass., so be sure to ask that before booking. Hope this helps....