I don't know about the other islands, but the stromness to hoy ferry is passenger only. I would imagine you could take a bike, but not sure. There is a ferry that takes cars across but it goes from a different port.

It is a fair distance down to the tombs on South Ronaldsay, if you're thinking of doing the journey down there several times during your stay then maybe Kirkwall is your best best, but if it's just going to be the once then I personally would still choose stromness. And of course you'd get to go past the ness twice on that journey, once in the morning and once in the evening on the way back. Need I say more? ;)

One other thing to consider - We went in July and everything was open, but if you are going in spring it might be worth checking facilities, ferries etc are all up and running.
Make sure you book for Maeshowe too, it was a timed ticket when we went, you can't just walk up and go in. Probably won't be an issue given the time of year, but better safe than sorry.