If I can get it locally, or it's an item they can order for me that I don't mind waiting for, I'll buy it from the fly shop. I do this with items like waders, wading boots, vests, reels, lines, etc..
If I need it now and they don't have it, I go where I have to in able to get it (I always tell them about it, as I want them to 'know' that if they'd carry what I wanted, I'd buy it from them...). Mostly this is tying supplies.
Price has little bearing on this. This is fishing, and we really 'need' none of this stuff. If I want a reel that's $600 at the fly shop and $300 on line, and I don't have the additional $300, I'll find a reel at the fly shop that costs the $300 (or wait until I have it all). It's only a fly reel, doesn't make that much difference one way or the other if I ever 'have' it.
Some folks think 'price' matters, though. Up to them.
Good Luck!
Buddy