I think FFG's book is better. FFG's books are almost always better than anyone else's, particularly AEG. Dungeons was okay but I never used it and sold it and most of my AEG books off because I wasn't getting enough use out of them (or any, in the case of Dungeons). Really, AEG comes out with most of these themed books first, then FFG comes along later and does a better version in hardcover for less money, LOL, and with much tighter editing. AEG has some of the worst editing of any publisher I've ever seen. MERCENARY and FEATS are AEG's best books, IMO, and the ones with the most to offer both players and DMs. I kept them!
AEG's GODS and MONSTER books weren't so hot (GODS being the better of the two, IMO, for all the new domains and monster PrCs). FFG's MONSTER HANDBOOK was far superior, as was WOTC's SAVAGE SPECIES. First isn't always better, in my experience with d20 publishers, it's often worse.
That said, I did not buy DUNGEONCRAFT for the same reason I sold AEG's DUNGEONS book off. I don't need a book to tell me how to create believable dungeons. DUNGEONCRAFT, to its credit, is much more than that, offering up new spells, PrCs, and information on how to live in, explore and build a dungeon. If I was going to buy a book on the subject, I'd buy DUNGEONCRAFT. It's pretty good, but one of FFG's weaker books, IMO. When I say weaker, I mean less useful. Were I DMing more and interested in building better dungeons, it would be more useful, but still not essential. It's a nice luxury item for those who can afford it.
I agree about MASTERCRAFT being a sweet deal at $4.95, but I already own most of the books previewed, and the ones I don't are ones I have zero interest in (MYTHIC RACES, SEAFARER'S HANDBOOK), so it's not something I'm gonna buy. I heartily recommend it to those short on cash and long on desire to own the full length books, however. Wish they'd managed to squeeze a preview of DUNGEONCRAFT in there, but I know how it goes (page count/cost, pushing "back catalog" product, etc.).