If you haven't already, check. http://www.aldenshoe.com/store.asp
The Tannery has stores in Harvard Square (Cambridge) and downtown on Boylston Street. Prices are full retail. You used to able to haggle them down, but they've stopped doing that. The selection in Harvard Sq is basically LWBs, PTBs, unlined chukkas, LHSs, and NSTs. They only have black and 8 shell as well as some calf. The selection at their Boylston store is more extensive but still nothing beyond the usual basics.
The J Crew Mens store in Copley has aldens as well, and Barneys has some also.
I spoke with a new retailer in the back bay area who said they want to carry Aldens but apparently they have a policy about how many stores in a given area can carry their shoes.
I thought it was BS, but when you think about it Brooks bros + J crew + Tannery + Barneys = 4 stores in a 4 block radius.
edit: As for the Tannery on Boylston; their make-ups are all pretty much stock but once in awhile they carry collabs with the Wilderness Workshop downstairs (so I've been told)
Thanks everyone for your input. I had forgotten I could check J Crew and Barneys as well. I know all the concerns about web orders from NRO but I recall someone saying their focus is really their B&M store and that it is a pretty nice store. I've also read some pretty negative reviews on the Tannery. But you have to take some of those with a grain of salt.