I would say it depends on your plans and whether or not you have much luggage with you. Getting from stansted to Dover by train will be around 3 hours as you have to go into and out of London. If you want to visit London beforehand anyway then it’s not so bad as you are breaking the journey. If you are just wanting to get to Dover and join the cruise then taking the ferry will mean less travel in the UK and you can also bring whatever baggage you like (Ryanair charge you per bag and have limited weight for each bag). However if you are arriving into the UK the day before your cruise there isn’t a lot to see and do in Dover. If you stay in London you have plenty of options and the fast train to Dover from London St Pancras is just over 1 hour.
If you do decide to fly then don’t limit yourself to Stansted. Heathrow, Gatwick, Luton and London City all have much better rail connections into London than Stansted and will get you there quicker.
