From Asakusa Tobu Station take the Tokyo Metro Ginza Line or Toei Asakusa Line to Shimbashi Station. From there take the Yurikamome Line to Ariake-Tennis-no-Mori (aka, Ariake) Station. Fare is 560 to 580 yen total and takes about 52 minutes on the Ginza Line and 47 minutes on the Asakusa Line. Exit west side of Ariake Station and head southwest and in a short distance there is a traffic circle of sorts with many buses. According to the website Uji provided above, there is a shuttle to the ferry port with a cost of 200 yen per person.
I would take either the 16:26 Ginza train or the 16:31 Asakusa train. This will get you to Ariake Station by 17:18. There is a shuttle departing at 17:30 and 17:50 to the port (according to the webpage). The earliest shuttle departure is 17:10. Travel time to the port is about 10 minutes.