'Entire' and 'whole' do seem to be exact synonyms, which is a pretty rare thing in itself. 'Entire' comes from a Latin root, while 'whole' has a Germanic source (originally meaning healthy/complete), so it does look like we have ended up with two words which do precisely the same job, and are interchangeable in all cases.
The only exceptions I could think of were set phrases such as 'on the whole' and 'as a whole', and constructions where 'whole' is used as an adverb, such as 'The snake ate the mouse whole'. Apart from that - feel free to use whichever word you wish!