I think I have subscribed to most of them at some point over the last two decades and I have enjoyed them all. Back in the eighties I got frustrated with Flyfisherman since their articles seemed to me to be too focused on the West but I have since returned to this mag and enjoy it. I also like Fish & Fly and Rod & Reel. I tried subscribing to Eastern Flyfishing for awhile. Although a good magazine, their definition of "eastern" was very broad and some of their articles were a bit too "kiss and tell" for my taste. They also published a couple articles, including one on the Letort, that I found contained misinformation.
Although not excusively fly fishing, some other favorites of mine are:
Shallow Water Angler
Gray's Sporting Journal
Sporting Classics
Florida Sportsman