It's a daytrip from Tokyo, therefore I'd like to plan ahead as I have limited time there.

From Irozaki I want to return to Shimoda by bus and spend the remaining evening there. Buses run quite frequently, so this shouldn't be a problem, right?

There are, however, still sightseeing cruises that make a round course around Irozaki. It lasts 25 minutes, costs 1200 yen and departs every 30 minutes. The website in Japanese:
http://www.izu-kamori.jp/izu-cruise/route/index.html

As for the bus between Shimoda and Irozaki, there is about one connection per hour and the one way trip takes about 40 minutes. Bus website in Japanese:
http://www.tokaibus.jp/

I didn't know about the holidays! I wanted to go on Sunday, because it said the sightseeing boat runs from Saturday to Monday only. But now this doesn't matter anymore, because the Irozaki sightseeing boat runs every day :)

Do you think if I go on FR, September 18th, I can avoid the crowds?

Again, thanks a lot for your help! :)

Uji and Georg,
I used to enjoy that boat ride quite a lot so in my shock I went to search for any information - unfortunately, yes, the Shimoda - Irozaki segment seems to have been discontinued.

Georg,
They have the Shimoda bay cruise, and also they still have the coast boat ride around Irozaki, as Uji mentioned - so you could take the bus to Irozaki, then take a boat ride along the rocky coast.