It depends on how much subway travel you’ll be doing. Ogikubo is west of the city proper and is at the end of a subway line, so you’ll be taking a lot of long-ish trips. Buying the two Keisei passes means you only have to do ~1360 yen of subway travel to break even, which seems doable.
That said, the JR Chuo and Yamanote Lines are just as useful getting from Ogikubo and around town, so doing the NEX round-trip ticket and buying a Suica/Pasmo fare card to take care of travel inside the city isn’t likely to end up costing that much more, assuming your day plans focus on one or two neighborhoods instead of jumping all over town, in which case the Keisei combo is a better deal.
Bus is the cheapest - Only 1000 yen each way from Narita to Tokyo.
I believe it’s only 220 yen from Tokyo to Okubo, you change train in Shinjuku (big station) that’s 1220 yen on the way. (For round, it’s 2440 yen)
When you travel around Tokyo, depending on where you visit, it could be metro or JR or Keisei and each have different 1 day pass. I wouldn’t go for pass. My friends from THAILAND purchased a day pass for Toei line before I met them but it was worthless since major sightseeing places were either located in JR or metro.