black Indys are available from the NYC Alden store. They are an awesome looking boot, I saw them in person while I was visiting there and the only thing that kept me from buying them was that I had just picked up the black Tanker boots from Context.
I think Leather Soul has some black Indy's in shell but I you would have to contact Tom.
Also, I have been wearing the hell out of Alden's for the last month and now my other shoe's and especially tennis shoes and running shoe's doe not feel right and hurt my feet. On the elliptical my running shoes are rubbing ans almost causing blisters. I am not sure if this has to do with the Alden's but it is annoying.