you should absolutely go down to Yokohama for a day if you got the time. It's quite a nice place with a vastly different vibe than Tokyo. The foreign influences can be felt at every corner and if you're into Jazz you'll love the night life.
I'd reccomend you just take the Toyoko Line (which turns into the Minato mirai line) from Shibuya and go straight to Minato Mirai. From there you can walk to moto machi and pass by all historic areas in almost a straight line.
If you're going with JR take the Keihin-Tohoku Line (turns into the Negishi line) to Sakuragi-Cho and walk from there (may be easier to find your way around). A good route would be something like train station -> Akarenga -> Osanbashi -> Chukagai (China Town) -> Motomachi -> Yamate (of if there's time you could also take the bus No.58,99 or 101 to bus station Honmoku to get to Sankeien, which is a nice Park)
On your way you pass by 2 Museum Ships and the Yokohama History/Wharf/Harbor Museum, I found all of them to be quite interesting, but If I had to pick one, I'd probably go with the NYK Hikawamaru.
To go back to Tokyo you can just take the Minato-Mirai Line from China Town back to Shibuya or JR from Motomachi
And if you've got some money to spare... you could also stay a night at the Yokohama Royal Park Hotel. As I said in an early post... waking up on the (up to the) 69th floor is not something you can do every day. the standard rooms aren't even that expensive, although it's the corner rooms where it's at.
https://www.booking.com/hotel/jp/yokohama-royal-park.en-gb.html