I like them as Good/Neutral aligned because it presents a fairly significant moral dilemma for non-Evil players, especially Good-aligned players, to harvest Eagle stones from them, or perhaps even use them. "You can revive the slain innocent child, but you must slay a noble creature to do so" sort of thing.
A few other things sometimes attributed to Thunderbirds in mythology:
Massive size: I've heard parallels with the Roc for how amazingly big some can get ('blot out the sun'). Certainly something for the "Elder" category I think.
Human form: I came across a myth once that said Thunderbirds could take human form by shedding their feathers like a blanket. The downside of course being that they couldn't return to their birth form if it was stolen from them. I doubt that it could turn anyone other than the true owner into a Thunderbird, but it's another potential magic item. The biggest trick is that it has to be stolen while the thunderbird is in human form since no one except the thunderbird themselves can 'remove' it in this fashion.