It's been several years since that first trip. I called, and spoke to the ranger who was in charge (sort of) of the water quality issues. Based on his unofficial recommendation, I took the MSR Miniworks, because it was within the recommendations and because it could be cleaned in the field. (There's no bailing out and going back to the car for a spare element at Isle Royale.) The other filters he recommended were the MSR Waterworks (?), which is no longer made, and the two Katadyn ceramic-element filters: Pocket and Mini. I think the Sawyer filter I use now meets their recommendation for pore size. It's backflushable, and the extreme light weight would allow you to carry a backup without too much trouble.

Don't be afraid to call the rangers on the islands with questions. They're nice, and very helpful. Also visit the national park website and download a copy of the island "newspaper," which has a lot of good info.