The AE's, I would say give them a call. They have *amazing* customer service, especially compared to Alden, and I feel confident that so long as you're positive you haven't abused them or caused it yourself somehow, they will make it right for you with a minimum of fuss and hassle.
The Aldens, sucks that there's no J Crew there. If Alden doesn't take care of it, you might be able to work something out with the original seller to have him swap the boots, maybe? It's a long shot but if your alternative is just stitching it and hoping nothing else is wrong... just food for thought. Alden seems to just stitch stuff like this up, doing a better job than your average cobbler I would imagine!