Normally and for a day, it would be best to stay near the major JR stations such as Tokyo or Shibuya, if you will be taking the JR NEX airport train. Any further south/east around the JR Yamanote loop line and you may be spending too much time transferring between train or metro.

Tokyo Station's basement food streets and the Daimaru store should be a good start. Hotels in the area tend to among the best and priciest, especially further north into the Marunouchi district. Shibuya is a bit less pricey but further away, the area around its famous crossing is great for night time foraging under the neon lights, if that's your thing.

Or you could try Ueno, since the Keisei Skyliner fast airport train goes straight there. From what I've seen, the station complex and surroundings are chock full of eats and widgets like the areas around Tokyo and Shibuya stations and there are more budget hotel options.

You're moving light, so an alternative would be to transfer from the NEX to the Yamanote line for the next-stop Yurakucho station. This brings you to Ginza's foodie establishments and department stores like Mitsukoshi, plus there's the late-night bar resto scene under the station's elevated tracks. You can readily reach JR Akihabara Station in a few minutes from any of these stations.

If you want to be closer to Tsukiji's street sushi action while still being proximate to Ginza, you could head to Higashi-Ginza Station on the Asakusa line, using the infrequent Keisei SkyAccess slow airport train. Many less pricey hotels and airbnbs are clustered there.