Thanks for the replies. I just want to be able to take some time after my plane gets in in the morning to tour Lisbon some without having to cut it short just to check-in and then go back out. I may be so tired that it won't matter much, but I would like the option. 3:30pm is about as late as I would even consider a check-in.
My plan is to taxi to the port from the airport, drop off my luggage, then pick up a hop-on hop-off bus and kick around as long as I can (or am awake for).