That was the problem with my current ship. Here are the steps I took in finding scale:
1. I figured that the average human height is 5'8" (The smaller the person, the bigger the ship will be)
2. I lied down next to a row of 1x1 blocks and counted the number of them it took to equal my length.
3. I did the same for block height.
In the end, I rounded and assumed that the width of a 1x1 brick is 1 foot, and the height is 15 inches. With this, I simply made the ship's framework 883 bricks long. For the height of say... a deck, I took the 8 feet, multiplied by 12, and divided by 15.
I hope this helped.