First of all I think "A.M." is a bit underrated. It's not as ambitious as any other Wilco album and the songwriting is still locked in that country/rock mode (like a less adult contemporary Eagles, or more charitably, like a more rock-oriented Gram Parsons). But it has some gems. I'd rather listen to "Casino Queen" or "Box Full of Letters" than most of "Wilco (the album)" (which I found pretty dull and not particularly well-written, compared to "Sky Blue Sky").

Second, yeah they have a great discography. Here are the other bands that come to mind:

Radiohead. Gotta give them props for "OK Computer," "Kid A" especially. I also love "In Rainbows" and "Amnesiac," and to a lesser extent "The Bends." On the other hand if you look at things album by album -

A.M. > Pablo Honey
Being There > The Bends (barely)
OK Computer > Summerteeth (it pains me to say so, because I love Summerteeth)
Kid A = Yankee Hotel Foxtrot
A Ghost is Born > Amnesiac
Sky Blue Sky > Hail to the Thief
In Rainbows > Wilco
The Whole Love > King of Limbs

I have Wilco coming out ahead here. This might not be the best way to compare two bands, but it looks to me like Wilco started stronger, is finishing stronger (perhaps - jury's still out), and had a roughly equivalent prime. If it wasn't for the high esteem in which I hold "OK Computer," I actually think Wilco would be the OBVIOUS choice.

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Modest Mouse. "Lonesome Crowded West" through "We Were Dead" are all classics or near-classics to me; they had their abrasive, quirky indie record to end all abrasive and quirky indie records; then an album moving somewhat into accessibility without getting commercial about it, and every bit the equal of its predecessor; then the improbable breakout success record which still managed to be really good (though it has a few filler tracks); and finally a worthy follow-up to that, showing that they know their lane well and could ride in it for a while if they choose. The big problem is that their earlier albums pre-"Lonesome" all kind of blend together. I like some stuff on all of them (especially "This is a Long Drive") but they are all the work of a band still finding itself. So half their discography is great to me, the other half not so much.

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Flaming Lips. They have more bad or average albums than any of these other bands (all their early stuff, pre-1990). But they also have three classics (The Soft Bulletin, Yoshimi, and Embryonic); two near-classics (Transmissions and Clouds Taste Metallic); a couple of very good albums (Hit to Death and Priest Driven Ambulance); a wild experiment that actually has good songs on it if you put forth the effort (Zaireeka); a latter-day clunker, a la "Wilco" or "King of Limbs" (At War With the Mystics); and a just-for-fun take on a classic album by another band (Dark Side of the Moon). Basically I would argue that their highlight reel is as strong or nearly so compared to Wilco and Radiohead, and due to being more prolific it's easier to give them leeway on a few bad albums, because they made up for it with so many good ones.

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And here's where I don't mention a few extreme metal bands, because no one will know or care what I'm talking about. (Except Jakob of course.)