When I first came to Japan there was a terrific ferry route from Tokyo to Kushiro, passing through some very productive water south of Hokkaido and with the added benefit of landing you close to the birding action in the east of the island. No long drive/train journey across the island required as when getting dumped in Tomakomai; even if that does get Magpie for your trip list. With that option long gone we old-timers get the chance to bore everyone else about the good old days.
Nowadays there are two long distance routes to Hokkaido from Honshu on the Pacific coast, from Nagoya (better for Short-tailed Albatross at the right time of year) and Oarai (convenient from Tokyo). There are also a couple of shorter distance ferries which might be of interest, the best being the Hakkodate to Oma taking 90 minutes to cross the Tsugaru Straits (three sailings per day) which might be worthwhile if you found yourself in the area with a day to spare. The Japan Sea routes are less productive and the only ferry I've used (Tsuruga-Tomakomai) had very limited viewing options.
As I'm based in Kyoto the Nagoya-Tomakomai route operated by Taiheiyo http://www.taiheiyo-ferry.co.jp/english/koro/tomanago.html is conveniently only 35 minutes away by shinkansen and I've used this in every month. The biggest drawback is that it passes through productive water off Iwate at night in both directions. So for summer breeding oceanodroma petrels the Oarai ferry would be better.
Nagoya-Tomakomai ferries pass each other just south of Sendai.
Since the Fukushima nuclear power station incident many people come on deck to take this distant shot.
Approaching the entrance to Ise Bay towards the end of the southward trip.
Izu & Ogasawara
For many visiting birders the shorter ferry route to Miyakejima or Hachijojima in the Izu Islands http://www.tokaikisen.co.jp/english/ is a must-do as the return trip can be done in a day, whereas the Ogasawara ferry http://www.ogasawarakaiun.co.jp/english/, which also leaves from the Takeshiba Sanbashi terminal in Tokyo, takes too long for the vast majority of visitors.
High on the list of targets for anyone travelling down to the Izu Islands would probably be Short-tailed Albatross and Tristram's Petrel both of which are winter breeders (Tristram's might be possible year round) and Bulwer's Petrel which is a summer breeder. If sailing further south to the Ogasawara Islands, Matsudaira's Petrel, Bonin Petrel and Bannerman's Shearwater are all summer breeders. As Bryan's Shearwater is a winter breeder obviously that would be the time to try for it but perhaps the Iwo Islands would be a better bet if there were any way to get there in winter.
Once a year the Ogasawara ferry company operates a sailing around the Iwo Islands which brings within reach a range of species not normally seen in Japanese waters.
The Izu Islands ferry from Miyakejima.
The Ogasawara ferry docked on Chichijima with the much smaller Hahajima ferry behind it.
The Hahajima ferry leaving Chichijima.
The send-off from Chichijima for the Ogasawara ferry.
I've never used the long distance Ryukyu southern route ferries and can't say how productive they may be in different seasons. In the Yaeyama Islands the inter-island ferries are too fast to be useful for birding, though Masked and Brown Booby should at least be identifiable. The slow Ishigaki-Yonaguni ferry is good for Bridled Terns, noddies and boobies. Perhaps in winter there might be an outside chance of seeing a Senkaku Short-tailed Albatross?
Other ferries I use regularly are to Hegurajima and Mishima in the Japan Sea, though neither are terribly exciting and I would never take them for their own sake. Having said that Japanese Murrelet is quite regular between Mishima and Hagi.
Hagi port, start point for the Mishima ferry.
The Hegurajima ferry in the island harbour with the Noto Peninsular in the distance.
I've used other Japan Sea ferries to South Korea and Tsushima but neither of these routes produced much other than the expected Streaked Shearwaters. Nevertheless, I wonder if Aleutian Tern might be possible on those routes if the timing were right.