As mentioned before, I designed the garage and tucked the house on the side of that. 46 feet deep so I can leave the Denali connected to the MC all summer. Also have a floor drain and sink with both hot and cold water. Fully insulated and windows for at least some light. Also have attic access for off season 'stuff'. Add a shelf and bar to hang vests on behind the boat so you can easily hang things without getting in and out of the boat. I also added electrical outlets under the eaves for Christmas lights. All outdoor outlets are switched to inside so I don't have to go out and plug them in, or run too many cords. Put a lot of electrical outlets in the garage and basement. Cheap when building and you won't regret it. Add a fan above the boat if you store it there nightly. Really helps to dry it out after a day of skiing. Garage needs to be at least 26 feet deep so you can get around your boat. Deeper if you have a bigger boat. High basement ceiling are important. Most builders have forms for it and you just need to ask.
Put everything in the contract and try to estimate ahead what you will need for allowances and either remove those from the builder and do it yourself, or increase the allowance to line up with your estimates. Can't emphsize that enough.
36 inch wide stairways are great. I also made my stairs straight. Furniture movers love me for that. Also allow staight approach to the stairs for lining things up at top and bottom. A wall right at the bottom of the steps can be difficult.
Put undercabinet lights in you kitchen right away. Hard to wire in later.
Visit the site every day if you can. Changes are easy and usually inexpensive if done before things are closed in.
Be your builders best friend. Ask for his input on the design and for cost drivers. Some things that are expensive may not be important to you. Always be happy when you work with him and let him know how much you appreciate his work. He'll do extra for you. It really counts.
Good luck and keep us posted with photos as it gets going.