Flying from London City would probably be marginally quicker in your case, but LCY is closed from mid-day Saturday to mid-day Sunday (always has been - this was part of the terms of its planning permission), which is why you haven't found any later flights.

If you can't fly from LCY then the train is definitely the way to go. Travelling by train you'll be in Manchester before your flight from LGW or LHR has even taken off - journey time from Euston to Manchester Airport is less than three hours.

The only thing you need to watch out for - as it's a week-end - is engineering work. If there is engineering work along that line then part of your journey may be by coach which will add time to your journey. You can check on engineering work and planned line closures at www.nationalrail.co.uk.