No ferries, much too far. Best you could do is a cruise ship, but the only ones that tend to do HK - Yokohama are the ultra-luxury ocean liners like the Queen Elizabeth, and then only once a year.
If you have a lot of time there are some cargo lines that accept passengers. Cargo ship schedules are very flexible, you have to be ready to go when they say so.
There is a ferry from Busan, Korea to Fukuoka, Japan but you have to get to Korea first and then travel to the coast so it will probably cost the same overall.
US$700 return is not bad, a good seat sale might get it down to $500.
However, given the daily cost of living in Japan, can you afford the rest of the trip? It's not somewhere you go for a cheap holiday, that's Thailand.