As you say, a "vehicle" is a specific machine for transport. Aeroplanes and boats are also vehicles. It is a very general word. "craft" is used a little differently. Firstly, the word is sometimes used with other words to define a particular form of vehicle e.g. a hovercraft, an aircraft. "aircraft" is used as an uncountable noun to refer to aeroplanes in general. Less commonly, it can be used as a simple synonym for "vehicle" but this can sound literary, so be careful. I can't think of other usages right now, but I think I've given you the main ones.