Dim memories, 30+-year-old book; very dark illustrations, about a young boy who lives with his uncle or grandfather and his tall and sort of shady assistant/mad scientist. They build a boat/ark, there is a huge storm, and they wind up shipwrecked in a zoo.
I loved this book! I asked my dad, it was his book, and he found it. It’s called Uncle Louie’s Fantastic Sea Voyage