You should be fine. If they say 'after 3pm' that normally means the tour will end and you will be dropped off at the airport early enough to check-in, do TSA, etc. I'd be surprised if you weren't at Sea-Tac by 1:30 or so. Getting you to the airport early enough is really their main priority and they will likely shorten the excursion if they see time dwindling away.
Here is something else to consider...post-cruise tours often don't attract enough interest to make them profitable and they will cancel them. This has happened to me 3 times over the years.