The difference is that "incorporate" means to include as part of a whole, so you might say, for example, "beat the cake mixture well to incorporate the flour", whereas you would not use the word in something like "the price of the cruise includes your air fare to and from the port of embarcation".

James is right. Incorporate means that the "included" thing ALSO has some relation or connection with the rest. However, in many situations, either word might sound fine.

They basically mean the same thing; to make part as a whole.