As stated above, general rule for Alaska is at the gate. An agent working the flight is supposed to list you and they are supposed to be there 1 hour prior. Some small stations prefer you to list at the ticket counter (and in at least one case only allow that) but the larger ones only allow listing at the gate. The exception is you can list at the counter if checking a bag, although your position at the gate is supposed to determine your actual spot in line.