I recommend against getting a flight and hotel package- I stayed in 5 different hostels in Japan all under 35$ a night and they were really clean, quiet and fun, and an easy place to meet people. I stayed one night in a hotel after I got back to Tokyo late, and for over double the price I had the noisiest nights sleep just so I could have my own bathroom and a breakfast in the morning (many hostels in Japan are not open all night and close at 10pm). There is a nice hostel in Yoyogi but you're going to Yokohama... I think I remember meeting people who were staying in Asakusa and I dont think they liked it
I don't know is it's the same hostel though.
And about airports- Yokohama i really just an extension of Tokyo. Nartia, the airport, is not right in Tokyo. If I remember correctly it is about a 30$ train ride and 30 minutes to the city. I dont know how to get to Yokohama. When you typed in you wanted to fly to Yokohama, the computer knew you really meant Narita airport.