Been there, done that
I have been lucky enough to do just that with my work. The first time was because a meeting made me miss the fast ferry back, and I just happened to have my fatty with....so time to ride the beach! Rode south for over an hour, then turned back and rode the whole way with the sun setting over the lake. I was hooked.
Funny enough I have not ridden much of the beaches on the WI side of the lake. I think there is more/wider beach to ride on the other side of the lake. Prevailing winds and all. FYI: All beaches in Michigan are open to riding, even the state owned property. Actually the only beach land on all of the Great Lakes not open to riding is in the Wisconsin State Parks. A sad commentary if you ask me.
Anyway, I have ridden the SS Badger, from Manitowoc, WI to Ludington, MI. Huge old ship. Still runs on coal. More like a short 4 hour cruise. Lots to do on board. Also ~$30 cheaper each way IIRC. Though I have not ridden the beaches around Ludington so I don't have much personal input there. Though from the looks of Google Earth you should be able to ride right off the ship, jump on the beach, and ride the few miles north to Ludington State Park.
I have also ridden what I call the fast ferry, really the Lake Express, from Milwaukee to Muskegon, MI. It is a much smaller and faster boat. You cruise at 45mph. It is damn windy if you go on deck! It only takes 2 hours to cross. 2 1/2 hours from on to off the ship. Interior is like being on a really wide plane. Really nice for business. I know the beach here well. At Muskegon you go through an inlet to Muskegon Lake. You can ride north or south from Muskegon to your hearts content. Lots of beach. On the south side of the inlet where the ship enters the lake (south side) is a very popular and massive beach. I think over 20 sand volleyball courts set up. It is really popular in the summer and great for beach watching. This is also the place I took my first ride. Though I did it in October, so not too many swimsuits around then ;-) If you ride north around Muskegon Lake (there is a nice pedestrian bike path), you end up right at Muskegon State Park. You can even set up camp right on the inlet and watch the ships and ferry come and go. There is also a cool museum there with a war ship and the USS Silversides, a restored WWII submarine, and the Great Lakes Naval Memorial and Museum that is located at the inlet as well. You will sail past them on the ferry.
Really I don't think you can go wrong with a bike trip on either ferry. I have been trying to talk my family into doing the same trip. I think it would be a great way to spend a few days. I would stay over a couple of days if you can. Lots of riding to do, and lots of things to explore by bike, on the other side.
Also I think Bear and some others took one of the ferry's over this spring and did a brewery tour?