The Mega Shibuya location is one of the larger ones. It is also likely the most convenient shop for the casual visitor.

https://www.donki.com/en/store/shop_detail.php?shop_id=442

I like the Nakameguro location. It's impressive but much less crowded than the Shibuya or Shinjuku locations. I avoid the Shinjuku store - it's claustrophobic.

One of the Mega DonQ stores. Of course there are several normal stores in Shinjuku (small), but the big Shibuya store is pretty good. Even my local Mega DonQ is pretty good - as a seven story emporium I use it as a source of some goods my guests have trouble finding in central Tokyo (way out in the burbs).

If asking about non-Tokyo locations, please specify. They are all over the country and some are better than others (the one by Kyoto station is not a mega, nor the Nagano opposite the station or the Sendai one in the covered mall - just as examples.)

I assume OP wanted Tokyo locations since it's posted in the Tokyo forum. Anyway, you can go to Donki's site and search fro "Mega". It will show you the Mega locations. Use an online translator if necessary.

As a footnote, I was looking for something on Tuesday that I hoped would be at an inner city (Tokyo) mega store (checked two) and cam up blank. Specifically, aged Suntory whiskey.

My local (suburb) store usually has stock, but we didn't have time to make the trip as clients were returning to Australia early the following morning - a 4:30 start for me, 5 a.m. for them :)

Maybe the one close to Shimbashi under the highway got whisky.

Shimbashi - that could have been an option - thanks. After the sumo and returning to Shinjuku that would have made things quite late, but I'll hold that for next time.

As another note, the prices seem to be a huge amount higher than even a year ago. Still, my client managed to get the options he wanted for a 30% discount to his home market - two bottles - one of Hakyushu 12 and one of Yamazaki 12. The level the prices were a few years ago vs today is crazy - I'll stick with something tasty rather than the 100k yen - plus options that are available.

How are the duty free shops at the airports? Won't Suntory Whisky be cheaper there?

The airport is more expensive. (if they have it) - feed back from clients. Again, not unusual that "duty free" is nmore expensive than in the city.