See additional comments in my review.
The port of Haifa is nothing special and we spent very little time in the city. Our focus was Jerusalem and Galilee.
We arranged to have our own guide in Israel. We spent the night in Jerusalem which is something I'd recommend because with the limited time you have on a cruise. You don't want to spend anymore time than necessary driving back and forth to the ship. This was especially true for us because Haifa is about two hours further from Jerusalem than Ashdod is.
I believe having our own guide allowed us to see much more than if we were on a bus tour. We were able to set our own pace which allowed us to see more. It's well worth the extra money if this is your first and possibly only time in Israel.