As long as you are on board the ship at least 30 minutes prior to its departure time, you will be fine.
In fact, the later you check in, the fewer the people in front of you to make you wait in line.
We've shown up around 45 minutes before departure to find the check-in hall empty except for a few bored staff. "We've been expecting you!", said the check-in clerk. We were on board within about 5 minutes of arriving.
A good rule of thumb to make best use of your time on land is:
Get off the ship as soon as you are allowed to in the mornings*
Get on the ship as late as you can in the afternoons (including check-in). Don't be concerned about the last shuttle bus or the last tender back to the ship being full. They are quite the opposite by that time!
* After a 6:30 am arrival in Southampton, we took the train and were on the ground in London before 9:00 am, for a great shore day up in Town.