The National Geographic Society has long offered print indexes of their back issues for sale. They are available at www.nationalgeographic.com. Click on "Catalog Quick Shop", click on "Magazines", then on the picture of the catalogs. As you can see, the 100-year 1888-1988 issue costs $29.99, the 1989-1998 runs $15.95, and the yearly issues from 1995-2002 run $6.00 each.

The site's National Geographic Magazine page provides a free online archive of the online version's most recent eight years of publication, but of course this doesn't include all the articles in the print version.

The site also provides a remarkable index to all of the organization's publications, including their TV specials, their kids' magazine, their maps and their specialized publications, as well as the old faithful NGM. I haven't explored it thoroughly, but it appears to go all the way back to 1888, although you can limit your search to a certain range of years on the QuickSearch page, which also includes a very thorough Search Help guide as you scroll down. The Advanced Search allows search of up to three terms in up to three fields using boolean operators.

To get to this index, go to http://magma.nationalgeographic.com/ngm/0403/index.html and click on "archives" (on the left). Once you get there, look through the block of text titled "Getting Around". You will find a sentence that reads: "
If you would like to search the Society's full publications index, click here." Click there. :) It's the same link as in the paragaph above this one, for "QuickSearch page".

Another source:

If you have access to the online periodical index EBSCOhost Web, either at home or onsite through your public library, or through a friendly public school or local college or university, you can access searchable records of full-text (no pictures) articles of National Geographic from 1995 up until 3 months ago. (The delay is the publisher's restriction, to encourage sales. The lack of pictures: that's their bread and butter, so of course they will limit access very strictly to those.) This includes keyword search of the entire publication, as well as title, author and subject, and Boolean searches using up to three terms and operators. Abstracts of the articles in earlier issues are searchable in the same ranges going back all the way to 1888. It allows you to browse the contents of particular issues, too, which is something I'm not sure NGM's online index does. These are major articles only. Unfortunately, the little blurbs at the beginning of each issue are pretty much lost in the process.

The full-text articles may be printed for individual use, saved to disc, and emailed (not as a mass-mailing) with the institution's subscription to EBSCO.

EBSCO is the online replacement many libraries use for the big red bound volumes of the Reader's Guide to Periodical Literature. I'm not sure you're old enough to remember those, REB, but it will ring a bell with the tottering ancients among us. ;)

It's not one-stop, since you have to mess around to gather your indices, but it's a start.