If your house is 1,000 sqft then I doubt your garage is more than 400 sqft or 20 x 20. If you extend the rear of your garage by 5 feet, 5 x 20, then you will be right at 50%. With a 25' deep garage, you should be able to get your boat in if its not too big. Another option would be to add a rear door to the garage. At least 9-10 feet wide so you can put your boat on a slab out back. Other than that, I would go for the variance. They are granted all the time and your neighbors would rather have your stuff in the garage than out in the front yard, right?
Good luck,
OL