There are 2 main airports serving Tokyo -- Narita and Haneda , so be careful with that choice Narita was 45/60 minute coach ride from our hotel and Haneda a quick taxi ride 10 minutes. This was April 2019.
Yokohama port is 30 minutes minimum from Tokyo.
When we did our trip we had a package from a travel agent which included cruise flights hotel and 3 days in Tokyo with a Bullitt train ride and trip to Mt Fuji, I think Viator may do similar 2/3 days in Tokyo.