I will be travelling on this route in a couple of weeks, so I was wondering if there are any ferries that offer online check-in?
The Stockholm Tallinn ferry route connects Sweden with Estonia and is currently operated by 2 ferry companies. The Tallink Silja service runs up to 7 times per week with a sailing duration of around 15 hours 30 minutes while the St Peter Line service runs up to 1 times per week with a duration from 16 hr 30 min.
Neither line offers online checkin for that route.
While Tallink does have online check-in, it is only offered for Tallinn-Helsinki and Helsinki-Tallinn.
Does not appear to have an online option
As a frequent traveller with Tallink Silja it's very easy for me to answer this question.
You must get a physical paper key with a magnetic stripe for your cabin and to be able to pass the automatic gates at the terminal. You can get the key(s) either at the manned kiosks or using self-service machines.
There's no need to "check-in" before you get your key.
If you happen to loose your key you can ask the manned kiosks at the terminal or the reception (information) on the boat for a new one. You only have to show your ID and they're free of charge. Your old key will be instantly de-activated.
When leaving the ferry you can keep the key or throw it away - it's just paper.
Tallink offers online check-in and mobile check-in foc some daytime routes where you normally don't have a cabin. These routes include Helsinki-Tallinn, Åland related trips via Turku, Stockholm or Helsinki (no cabin) and Vuosaari-Muuga.
I also suggest downloading the Tallink Silja app for your phone and to give it your booking details. It'll send you useful notifications and will also give you a QR code you can use at the self-service kiosks to get your tickets with one click.