I took the Sea Hunter III from Grand Portage to Windigo. I think this is the only boat that will take you to Windigo and return on the same day. There are other boats that will take you and pick you up on a later day (Voyager II 2 hours one way) and the (Wenonah 3 hours one way). The people running the trip were not that friendly nor particularly helpful. Unfortunately, if you are going to Isle Royale from Grand Portage, there are no other options unless you have yout own boat.
There are two boats that go to the eastern end of Isle Royale. The Ranger III goes to Rock Harbor from Houghton and returns and takes 6 hours one way. The Isle Royale Queen IV goes from Copper Harbor (on the Keweenaw Peninsula) to Rock Harbor and back and takes 3 hours one way.
A day trip to the Islands west/south end. The Wenonah is the only boat that returns the same day. You can take the 3 hours (out) trip to Windigo. Here, you'll have 3 hours to hike, visit the nature center, take a guided walk and then the 3 hour trip back. On calm days (most), you'll have a chance to see the wreck of the America preserved in the cold waters of Lake Superior. There is always the Rock of Ages Lighthouse, which stands out on a reef beyond the tip of the island. Just of the lighthouse, is the 3-C's reef. Here, three ships (all starting with C, i.e., The Cox) ran aground in the 19th century. Each one lines beneath the waves. If the captain is talkative, expect recollections of the fishing industry of Lake Superior. His family has been in the business for nearly 100 years.
The Ranger III is the government boat. It provides service to the island 3 times a week. It takes 6 hours, so plan on a long sea voyage. There is limited food and beverage service and an extended view of the lake. The Ranger heads to Mott Island 1st, which is the park on island headquarters before turning into Rock Harbor for the night.
Much improved over the IRQ III, the IV cuts through the waves from Copper Harbor on Michigan's Keweenaw Peninsula. It also makes a round trip daily, but to Rock Harbor. You need to be there bright and early.
The Voyageur II is the only commercial boat that circles the island. It leaves from Grand Portage, Minnesota 3 days a week and circles the island with stops at Windigo, Rock Harbor and points inbetween. It gives you a great overview of the island and can be your one-way ride to another part of the island, for a day hike or overnight hike back.
You can also make the trip from Houghton by seaplane which only takes 30 minutes one way. The seaplane goes to Rock Harbor and Windigo. This is about $200 one way.
Many people arrive at Isle Royale using their own boats, or ones they rented. There are overnight docking areas all around the island. along with some that are available only for day trips.