I was in Chania in mid May on Oceania. Yes, you dock in Souda Bay at the ferry port a little north of the city. We and another ship docked there, so probably you will too. There was a shuttle from right outside port to the market, as described above. If you look on a map you'll likely see where the market is - large enclosed building, but closed for reconstruction when we were there. From there you can walk down to the waterfront, passing some shops (closed when we were there, which was a Sunday). When shuttle drops you (free for us, but 5 euros roundtrip (I think, or maybe $5, for the other ship) you will just go to main street there, turn left, and then right on cross street to head to the water. But you may want to check a map to make sure I remember things correctly! I went to the right and down, as I wanted to end up on the side of the waterfront that has the breakwater out to the charming lighthouse. I ended up at the other end of the waterfront, so walked back a different way - one that brought me back via a shopping street. There was a big map thingy posted so you could get your bearings, but I just set out to take my chances at getting where I wanted to get. And on the breakwater, if you go at least 5 minutes or so, you may see the mountains behind the town - with snow on them in May!
I enjoyed just exploring Chania. It's a very pretty city. To go back to the shuttle stop, I'd suggest downloading a Chania map from maps.me before you leave home. Once in Chania, assuming you have gps in your cell phone, you'll be able to pull up the map without wifi and see where you are, and where you want to be. Back to the shuttle stop location was a little confusing after I roamed around quite a bit along the waterfront and in the "Splantzia" district and more. Back at the stop, I had to wait maybe 5-10 minutes before a bus for the port, an Oceania-bound bus, appeared. If I had taken the one that came first, I suppose they may have asked for my ticket, as I was on the other cruise line. But the port is the port - so each bus was no doubt going same place. I think it was around a 15 minute ride from Chania to Souda port.
There are other things to do and see in that area like monasteries and a beautiful Greek (National?) cemetery, or the nearby city of Rethymno, with another lighthouse, and a bus from Chania. But I happily spent the morning, and then a couple hours after lunch, in Chania. In addition to maps.me, you may want to google the website of the segway operator in Chania. It was a helpful website, though the segway excursion was not available Sunday, so we couldn't take it. Also, if you go off on your own (to shuttle and town) and you leave by noon, it's possible there will be a tourist info person with maps stationed at the port. Someone was there until 12.30 when we were there, with a great map for people to grab, but I don't know if the person comes for all cruise ships or just when asked. (Oceania usually arranges that service if it's available.)
Whatever you do, hope you enjoy Chania. I found it to be a wonderful place to explore and take pictures. My pictures are in a photo gallery here if interested, but you'll have to find the Chania gallery:www.pbase.com/roothy123